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Background A few researches evaluated the association of polymorphisms at SERPINA5 and fat mass and obesity-associated protein (FTO) genes with papillary thyroid cancer (PTC) globally. Here, we examined the presence of genetic variations within coding exon 3 of SERPINA5 gene and FTO rs9939609 polymorphism in Iranian PTC patients. Methods A total of 122 patients (42 cases for SERPINA5 and 80 cases for FTO gene) and 120 healthy subjects (40 subjects or SERPINA5 and 80 subjects for FTO gene) were recruited. The genetic variation within coding exon 3 of SERPINA5 gene was evaluated by reaction-single-strand conformation polymorphism (PCR-SSCP) and FTO rs9939609 polymorphism was evaluated by RFLP-PCR assay. Results The PCR-SSCP technique detected two rs6115G>A and rs6112T>C genetic variations within coding exon 3 of SERPINA5 gene and approved also by direct sequencing. For rs6112T>C polymorphism seven patients was heterozygous and for rs6115G>A seven PTC patients were heterozygous and two patients were homozygous. Conclusion This study indicated that SERPINA5 rs6115G>A and rs6112T>C polymorphisms might be a novel susceptibility locus for PTC in Iranian patients. However, our findings do not support an association between FTO rs9939609 polymorphism and PTC risk.

Aim To describe two cases of intra-articular nodular fasciitis (NF) which developed within the knee joint and were associated with the expression of the MYH9-USP6 gene fusion. Patients and methods Two women, 30 and 56 years of age, with no history of joint disease or knee joint trauma, are presented in our cases. We report these cases describing the clinical presentation, assessment, histopathological examination, gene expression, and clinical management. Results Both patients presented with knee pain and limitation in the range of flexion. We diagnosed our two cases as intraarticular nodular fasciitis based on histological findings and by the detection of the MYH9-USP6 gene fusion. The transcript of MYH9-USP6 gene fusion was identified by RT-PCR and direct sequencing in both cases. Conclusion We report the first cases of intra-articular NF involving the knee joint, with identification of a MYH9-USP6 gene fusion by RT-PCR. NF should be considered in the differential diagnosis of intra-articular lesions.

Accurate genotyping is important to improve the treatment of hepatitis C virus (HCV) infection. We herein report a 44-year-old Japanese man with hemophilia A and coinfection of HCV and human immunodeficiency virus (HIV) who was diagnosed with HCV genotype 4 by direct sequencing. Two genotyping tests based on the nested polymerase chain reaction method that we used misdiagnosed his genotype as 2b and 1b. Although several HCV genotyping tests are available in Japan, it is important to recognize that some cannot detect genotype 4. Care should be taken when genotyping HCV patients who have received non-heated coagulation factor preparations or were infected abroad.

Pharmaceutical companies have increasingly utilized genomic data for the selection of drug targets and the development of precision medicine approaches. Most major pharmaceutical companies routinely collect DNA from clinical trial participants and conduct pharmacogenomic (PGx) studies. However, the implementation of PGx studies during clinical development presents a number of challenges. These challenges include adapting to a constantly changing global regulatory environment, challenges in study design and clinical implementation, and the increasing concerns over patient privacy. Advances in the field of genomics are also providing new opportunities for pharmaceutical companies, including the availability of large genomic databases linked to patient health information, the growing use of polygenic risk scores, and the direct sequencing of clinical trial participants. The Industry Pharmacogenomics Working Group (I-PWG) is an association of pharmaceutical companies actively working in the field of pharmacogenomics. This I-PWG perspective will provide an overview of the steps pharmaceutical companies are taking to address each of these challenges, and the approaches being taken to capitalize on emerging scientific opportunities.

This study describes molecular detection, high prevalence and geographical distribution of blueberry latent virus (BlLV) in Serbia. BlLV was discovered in the USA and the main signature of the virus is latent infection. A number of 110 samples from 14 highbush blueberry cultivars collected from different locations in 9 municipalities of Serbia were tested by RT-PCR with BlLV-specific primers. The presence of BlLV was confirmed in 69 samples (62.7%) in all surveyed locations. BlLV was confirmed in single infections, but also in a mixed infection with blueberry mosaic-associated virus and blueberry red ringspot virus. To access the genetic diversity, direct sequencing of the fragment from the fusion protein gene of 14 Serbian isolates was done. Serbian isolates showed 99.64–100% nucleotide (nt) and 98.94–100% amino acid (aa) identity. In comparison with the available BlLV sequences of the isolates from Bosnia and Herzegovina, Japan, South Korea and the USA, our isolates showed 99.29–100 nt and 97.87–100% aa similarity.

Marfan syndrome (MFS) is a heritable connective tissue disorder (HCTD) caused by pathogenic variants in FBN1 that frequently occur de novo. Although individuals with somatogonadal mosaicisms have been reported with respect to MFS and other HCTD, the overall frequency of parental mosaicism in this pathology is unknown. In an attempt to estimate this frequency, we reviewed all the 333 patients with a disease-causing variant in FBN1. We then used direct sequencing, combined with High Resolution Melting Analysis, to detect mosaicism in their parents, complemented by NGS when a mosaicism was objectivized. We found that (1) the number of apparently de novo events is much higher than the classically admitted number (around 50% of patients and not 25% as expected for FBN1) and (2) around 5% of the FBN1 disease-causing variants were not actually de novo as anticipated, but inherited in a context of somatogonadal mosaicisms revealed in parents from three families. High Resolution Melting Analysis and NGS were more efficient at detecting and evaluating the level of mosaicism compared to direct Sanger sequencing. We also investigated individuals with a causal variant in another gene identified through our “aortic diseases genes” NGS panel and report, for the first time, on an individual with a somatogonadal mosaicism in COL5A1. Our study shows that parental mosaicism is not that rare in Marfan syndrome and should be investigated with appropriate methods given its implications in patient’s management.

Objective The genetic hallmark of CML is known as the appearance of t(9;22)(q34.1;q11.2) (BCR-ABL1) which is present in more than 95% of cases. Here, we demonstrated practical laboratory tools for monitoring of BCR-ABL1 transcripts in chronic myeloid leukemia patients undergoing TK inhibitor therapy. Methods Real time quantitative PCR and direct sequencing were performed for monitoring of BCR-ABL1 transcripts in 245 treated CML. Results At month 3 after first time point of monitoring, we found that 89% (218/245), 2% (5/245), and 9% (22/245) of patients are determined as optimal, warning, and failure response, respectively. The responses to TKI were slightly decreased at months 6 as following 73% optimal (180/245), 18% warning (43/245), and 9% failure response (22/245). Additionally, responses to TKI were gradually decreased at month 12 after first time point of monitoring as following 65% optimal (160/245), 13% warning (31/245), and 22% failure (54/245). We could detect 20% (49/245) of patients positive for BCR-ABL1 TKD mutations. Interestingly, one third (17 of 49) of TKD mutated cases were positive for compound/polyclonal mutation patterns. While major molecular response were observed in the majority of patients without TKD mutation, resistant to TKI were detected in patients with T315I mutation (n = 9; % mean IS = 8.1510, % median IS = 9.7000), compound/polyclonal mutations with T315I (n = 9; % mean IS = 13.0779, % median IS = 5.404), and other TKD mutations (n = 14; % mean IS = 8.1416, % median IS = 1.060), respectively. Conlusion: These practical laboratory techniques provided a more comprehensive understanding of CML progression during drug therapy and could be of benefit in earlier prognosis.

Norovirus (NoV) is one of the most important viral causes of acute gastroenteritis (AGE) in children worldwide. Only a few studies have reported AGE with NoV-positive in some cities in Indonesia. This study aimed to investigate the incidence and clinical characteristic of NoV infection, and also genotype distribution of NoV in children with AGE in Jambi, as the capital and the largest city of Jambi province, Indonesia. Stool samples were collected from children (≤15 years of age) with AGE at three participating hospitals in Jambi from February to April 2019. The detection of NoV and its genotyping were carried out by reverse-transcriptase polymerase chain reaction and direct sequencing. Of the 91 stool samples collected, 14 (15.4%) were positive for NoV. Fever, vomiting, and severe diarrhea were commonly observed in AGE with NoV, while level of dehydration was statistically significant difference between children with NoV-positive and those with NoV-negative. The most prevalent genotype was GI.4 (42.9%), followed by GII.6 (28.6%) and some other genotypes. Interestingly, this study found the predominance of GI.4, differed from previous reports in Indonesia. Continuously investigation of the circulating genotype is needed to control the NoV-infected AGE.

Background and object The risk of occult HBV infection (OBI) in children whose mothers are HBV carriers has received more widespread attention, but there were few reports to focus on the children with HBsAg-positive parents. In this study, we aimed to investigate the prevalence of OBI in immunized children with HBsAg-positive parents. Methods HBV-vaccinated Chinese hospitalized children with HBsAg-positive parents were analyzed in our investigation. Eligible subjects were tested using a standard nested PCR for all HBV genes, and analyzed by direct sequencing. Results There were 327 HBsAg-negative children included in the study out of about 9800 involved HBV-vaccinated hospitalized children. The positive rate of OBI was 3.1% (10/327) in the eligible children and 14.1% (46/327) with HBV DNA detectable. No significant differences were found between one and at least two regions positive groups (p > 0.05). The proportions of HBV DNA detectable in children with HBV father-carriers and mother-carriers were similar. The risk factors for HBV DNA-positive children could be male, anti-HBs levels, and anti-HBc positive. Conclusion There are 3.1% of OBIs and 14.1% of suspected OBI in vaccinated children with HBsAg-positive parents. The potential risk of suspected OBI in children with HBsAg-positive father should not be ignored. Anti-HBc positivity may be a useful seromarker for suspected OBI screening in vaccinated children. To prevent HBV breakthrough infection, accurate and convenient method is needed to detect OBI timely and exhaustively. Electronic supplementary material The online version of this article (10.1007/s12072-020-10055-9) contains supplementary material, which is available to authorized users.

ELANE-related neutropenia includes severe congenital neutropenia and cyclic neutropenia. Both are clinically characterized by recurrent fever, skin and oropharyngeal inflammation. We report a novel mutation in ELANE in a 20-year-old man with a history of self-limiting febrile episodes and neutropenia with a cyclic pattern since 7 years of age. Direct sequencing analysis of ELANE revealed he was heterozygous for a novel missense mutation (p.Ala57Asp). The Ala57 residue is a mutation hotspot, and all previously reported missense mutations (Ala57Ser/Thr/Val) were observed in severe congenital neutropenia cases. Thus, the present case demonstrates a phenotypic variability in ELANE-related neutropenia from mutated Ala57.

Purpose: To evaluate the effect of methylenetetrahydrofolate reductase (MTHFR) polymorphism on toxicity in gastric cancer (GC) patients treated with capecitabine. Methods: One hundred and twenty-six GC patients were treated with capecitabine in the study. DNA from GC patients was genotyped for MTHFR A1298C using direct sequencing. Toxicity evaluations were graded. Clinical response was assessed. Results: In 87.3 % of the patients, capecitabine toxicity was observed. As for MTHFR A1298C polymorphism, 55.6 % patients who exhibited it were associated with reduced MTHFR activity. MTHFR A1298C was associated with capecitabine-related toxicity (p = 0.008); in addition, MTHFR A1298C was significantly associated with gastrointestinal toxicity (p = 0.026), but not with other types of toxicity. Conclusion: The findings suggest that MTHFR A1298C may be useful for predicting toxicity in GC patients receiving capecitabine treatment, especially gastrointestinal toxicity. Keywords: MTHFR, Polymorphism, Gastric cancer, Toxicity

Background ABO blood system has many subgroups. In A group, A1 phenotype and A2 phenotype are more common, and A2 is caused by deletion or substitution in A1 allele (ABO*A1.01). Methods Based on standard ABO serological test, the subject was identified as A2 phenotype. Direct sequencing and ABO gene cloning were performed to analyze the allele. Results The subject had one A1v allele (ABO*A1.02) and one O allele. The haplotype sequencing analysis of each allelic clone demonstrated that allele 1 was A1v (ABO*A1.02) allele with nt543 variation (543 G > C) and allele 2 was O1v allele (ABO*O.01.02) with nt261 deletion and nt220 variation. Conclusion The 543 G > C nucleotide substitution of the present A1v allele (ABO*A1.02) shares the same sequence variation site with Ax allele (ABO*AW.33) (543 G > T), and both 543 G > C and 543 G > T nucleotide substitutions encode the same amino acid change of tryptophan to cysteine. Mechanism, such as allelic enhancement, has been proposed to explain this controversial phenotype-genotype relationship. But in present case, there has been no B allele to enhance the expression of Ax to that expected of A2, so there could be another novel underlying mechanism to be investigated.

Background Epigenetic markers such as DNA methylation of the monoamine oxidase A (MAOA) gene have previously been shown to be altered in anxiety- and stress-related disorders and to constitute a potential mechanism of action of psychotherapeutic interventions such as cognitive behavioral therapy in these disorders. The present study for the first time, to our knowledge, investigated MAOA methylation in patients with obsessive-compulsive disorder applying a longitudinal psychotherapy-epigenetic approach. Methods The present sample comprised 14 unmedicated female patients with primary obsessive-compulsive disorder and 14 age- and sex-matched healthy controls. MAOA promoter methylation was analyzed via direct sequencing of sodium bisulfite-treated DNA extracted from whole blood before and after an 8- to 10-week semi-standardized, obsessive-compulsive disorder–specific cognitive behavioral therapy. Clinical response was assessed by means of the Yale-Brown Obsessive Compulsive Scale. Results Significantly lower MAOA promoter methylation was discerned in obsessive-compulsive disorder patients relative to healthy controls. Data were available for 12 patients with obsessive-compulsive disorder and 14 controls. Furthermore, following cognitive behavioral therapy, clinical improvement, i.e., decreases in obsessive-compulsive disorder symptoms as indicated by lower scores on the Yale-Brown Obsessive Compulsive Scale was found to be significantly correlated with increases in MAOA methylation levels in patients (data available for n = 7). Conclusions The present pilot data suggest MAOA hypomethylation as a potential risk marker of obsessive-compulsive disorder and an increase in MAOA methylation levels as a possible mechanistic correlate of response to cognitive behavioral therapy in obsessive-compulsive disorder.

Hypomyelination and congenital cataract (HCC) is characterized by congenital cataract, progressive neurologic impairment, and diffuse myelin deficiency. This autosomal recessive disorder is caused by homozygous variant in the FAM126A gene. Five consanguineous Tunisian patients, belonging to three unrelated families, underwent routine blood tests, electroneuromyography, and magnetic resonance imaging of the brain. The direct sequencing of FAM126A exons was performed for the patients and their relatives. We summarized the 30 previously published HCC cases. All of our patients were carriers of a previously reported c.414 + 1G > T (IVS5 + 1G > T) variant, but the clinical spectrum was variable. Despite the absence of a phenotype–genotype correlation in HCC disease, screening of this splice site variant should be performed in family members at risk.

Transient antenatal Bartter syndrome due to melanoma-associated antigen D2 gene mutation is a newly reported type of Bartter syndrome. Its characteristics include an X-linked inheritance pattern, early-onset hydramnios, and spontaneous disappearance of symptoms after childbirth. To date, there have been no reports of prenatally diagnosed cases. We herein present the case of a preterm male born to a mother with early-onset hydramnios and a family history of X-linked idiopathic hydramnios. We suspected melanoma-associated antigen D2 gene mutation and performed direct sequencing. As a result, we were able to prenatally establish a diagnosis of transient Bartter syndrome due to a melanoma-associated antigen D2 gene mutation.

Rat-bite fever caused by Streptobacillus moniliformis is a rare infection that may be fatal. An adolescent male presented with multiorgan failure, negative blood cultures and Gram-negative rods in blood smear. S. moniliformis was identified by 16S ribosomal RNA gene sequencing from the blood. He developed systemic hyperinflammatory syndrome resembling hemophagocytic lymphohistiocytosis, for which immune-globulins and steroids were added to the antibiotic regimen and he rapidly recovered.

Purpose This study was performed to clarify the clinical features of Japanese patients with PRRT2 mutations. Methods The PRRT2 gene was analyzed in 135 patients with benign infantile epilepsy (BIE) or paroxysmal kinesigenic dyskinesia (PKD) using a direct sequencing method: 92 patients had BIE alone, 25 had both BIE and PKD, and 18 had PKD alone. Of the cases, 105 were familial, and 30 were sporadic. Clinical information was collected using a structured questionnaire. Results PRRT2 mutations were identified in 104 patients. Among the familial cases, PRRT2 mutations were found in at least one individual in 21 of 28 families with BIE alone, in 26 of 27 families with infantile convulsions and choreoathetosis, and in 2 of 3 families with PKD alone. Among the sporadic cases, PRRT2 mutations were observed in 7 of 25 patients with BIE alone, in 1 of 1 patient with BIE and PKD, and in 3 of 4 patients with PKD alone. The c.649dupC mutation was the most frequent, followed by the c.981C > G mutation. Among the patients with epilepsy, the median age at BIE onset was 5 months, the median age at the last seizure was 6 months, and the median number of seizures was 5. Conclusion PRRT2 mutations were found in 68% of Japanese probands with BIE or PKD. The phenotypes of BIE associated with PRRT2 mutations were consistent with those of BIE diagnosed clinically.

Background CRTC1-MAML2 fusion is often detected in low- or intermediate-grade salivary mucoepidermoid carcinoma (MEC), and it is associated with a favorable clinical course. Primary MEC of the liver is an extremely rare, aggressive tumor, and no study has investigated CRTC1-MAML2 fusion. Case presentation A 79-year-old Japanese female presented with an approx. 5-cm hepatic mass lesion. We surgically resected the lesion under the clinical diagnosis of intrahepatic cholangiocarcinoma. The histological and immunohistochemical findings were consistent with high-grade MEC, consisting of squamoid, mucin-producing, and intermediate tumor cells. Our RT-PCR analysis revealed the presence of CRTC1-MAML2 fusion. This fusion gene was further confirmed by direct sequencing. The patient is still alive almost 10 years after the surgery. Conclusion This is the first case report of primary MEC of the liver with CRTC1-MAML2 fusion, with long survival. The present case has significant implications for the entity of primary MEC of the liver which should be distinguished from adenosquamous carcinoma.

Chronic myeloid leukemia (CML) patients who have BCR-ABL T315I mutation, usually present in the advance phase of the disease with overall survival (OS) shorter than those without the mutation. This study aimed to determine the prevalence of T315I mutation amongst imatinib mesylate (IM) resistant CML patients and to compare the OS between T315I-mutated and non-T315I-mutated patients. Sixty consecutive CML patients who were treated with IM for at least 18 months and their treatment responses, were recorded. The mutation analysis was done using allele-specific oligonucleotide reverse transcriptase-polymerase chain reaction (RT-PCR) assay followed by direct sequencing technique. Forty-two patients (70%) were found to have IM-resistance. Five out of 42 patients had detectable T315I mutation. Median OS of IM-resistant T315I-mutated patients was 96 months (95% CI:54-138) compared to 84 months (95% CI:48-120) in non T315I-mutated patients, although this was found to be statistically insignificant (p = 0.43). The present study showed a higher prevalence of T315I mutation as compared to a few local studies. Median OS of T315I-mutated patients were observed to be longer than non-T315-mutated patients. Further studies encompassing larger cohort of patients are required to confirm this finding.

Background and Aims: Metabolic abnormalities in T2DM (Type 2 diabetes mellitus) include classic manifestations such as impaired insulin secretion, synthesis and peripheral insulin resistance. The intronic variants rs7903146 and rs12255372 of the TCF7L2 (transcription factor 7-like 2) gene are strongly associated with risk of incidence of T2DM and impaired β-cell functions. Studies addressing the early T2DM onset, and early insulin dependence in T2DM patients of south Tamil Nadu are still lacking, and hence the present study focuses in determining the influence of the TCF7L2 polymorphisms in the incidence and disease course in the T2DM patients of south Tamil Nadu. Methods: Anthropometric measurements and biochemical parameters were carried out in early onset (Group A), early onset insulin dependent T2DM patients (Group B) and non-insulin dependent T2DM patients (Group C). PCR, allele specific PCR (ASP), PCR product sequencing strategies were utilized to determine the genotype and the impact of the TCF7L2 SNPs in the T2DM disease course. Results: Female T2DM patients with the CT/TT rs7903146 genotype (P = 0.005) and the rs12255372 GT/TT genotype (P = 0.036) exhibited a significantly low mean age for T2DM incidence. Correlation/regression analysis in the T2DM patients revealed that rs12255372 (P = 0.042) is associated with early onset in the Group C patients and the rs7903146 (P = 0.018), rs12255372 (P = 0.026) are associated with insulin dependence in the group B patients. Conclusion: Screening for the TCF7L2 polymorphisms will prevent T2DM incidence and enable life style changes, appropriate therapeutic strategies that would help combat the accelerated disease course in the T2DM patients.

Background: The incidence of mixed hepatitis C virus (HCV) genotype infection is variable, and a few reports exist regarding the efficacy of direct-acting antivirals (DAA) therapy for mixed genotype. We aimed to investigate the prevalence of mixed genotype and its impact on the virologic response to DAA therapy. Methods: A total of 365 patients with chronic HCV infection who completed antiviral therapy were recruited. Nested polymerase chain reaction with universal and specific primers of genotypes 1b and 2 and direct sequencing were used for HCV genotyping. Results: Direct sequencing with universal primers defined genotypes 1b (n = 230), 2a (n = 95), and 2b (n = 40). Direct sequencing of genotype 2 was performed in patients with genotype 1b, and direct sequencing of genotype 1b in patients with genotype 2. Four patients with genotype 1b underwent amplification for genotype 2, and direct sequencing identified genotypes 1b (n = 1), 2a (n = 1), and 2b (n = 2). None with genotype 2 underwent amplification for genotype 1b. Three cases were confirmed to have mixed genotype. Conclusions: Mixed genotype was rare, and hence the impact of mixed genotype on treatment outcome with DAA therapy is expected to be minimal.

Aim. In this research, we aim to develop a criterion for differentiating MutYH-associated polyposis from sporadic colon polyps.Materials and methods. A search for mutations in the MutYH gene was carried out using the PCR, electrophoresis and direct sequencing methods among the following groups of people: 18 patients under 45 years old with more than 100 polyps diagnosed in the large intestine; 86 patients over 45 years old with 4–100 polyps; 150 people of the control group.Results. Mutations in the MutYH gene were detected in 2 out of 18 patients having more than 100 polyps. Among 86 patients with 4–100 polyps, mutations were found in 10 people having more than 20 polyps. Mutations in the MutYH gene were not detected in patients with 4–19 polyps (p Conclusion. For the first time, the lower limit of the polyp number has been established, allowing the MutYH-associated polyposis to be differentiated from sporadic polyps.

Prevalence of inhibitors in Afghan hemophilia patients has not been reported previously. Our aim was to determine the prevalence of factor VIII inhibitors among hemophilia A patients from the Kabul province of Afghanistan to identify and characterize the pattern of inhibitor formation. Clinical information and blood samples were collected from three hemophilia centers in Kabul, Afghanistan. Plasma samples were obtained from 62 patients with severe (80.5%) and 15 patients with moderate hemophilia A (19.5%) in this cross-sectional study design. All the patients were receiving on-demand treatment. The Nijmegen modification of the Bethesda assay was used to detect inhibitors. Multiplex PCR, inverse-PCR, Multiplex ligation-dependent probe amplification and direct sequencing were performed for genotyping. Inhibitor activity was detected in one out of 15 (6.7%) patients with moderate hemophilia and in six out of 62 (9.7%) with severe disease. Apart from the intron 22 inversion, five different mutations including one missense, two large and two small deletions were detected. This is the first report showing that the prevalence of inhibitors in Afghan hemophilia A patients is much lower than in other populations.

Genetic screening paradigms for the nephrotic syndrome (NS) in the developed world are well established; however, screening in developing countries has received only minor attention. We retrospectively analyzed a cohort of all children who underwent genetic testing for challenging NS from our registry in the 10-year interval from 2000 to 2010 and based on 58 patients aged 0–12 years with at least one of the following clinical diagnosis: Nonsyndromic steroid-resistant nephrotic syndrome (SRNS), familial NS, and congenital NS. Of these, 23 patients (~40%) had a history of familial disease occurrence. All cases were screened for NPHS2 and WT1 mutations by direct sequencing of all exons of the genes. In addition, all patients who were diagnosed during the first three months of life were screened for NPHS1 mutations too. A genetic disease cause was identified in 12 patients (20.7%); of these, five novel mutations, all in NPHS2 accounting for 42% of all mutations and 9% of the cohort. Nine patients were found to have NPHS2 mutations. Only one case with SRNS had a mutation in WT1. Of the five congenital NS, two cases were found to have NPHS1 mutations and one case with NPHS2 mutation. Therefore, mutations in NPHS2 were the most commonly identified and explained in 15.5% of the screened patients and WT1 mutation in 1.7% of cases, whereas NPHS1 mutations were found in 40% of congenital NS cases. A genetic disease cause was identified in 20.7% of the screened patients. Among 12 identified mutations, abnormalities in NPHS2 (n = 9) were most commonly identified.

Background The Met136Val mutation in SCN8A was described in a case of trigeminal neuralgia but no frequency among affected individuals was provided. Methods Direct sequencing of 123 individuals diagnosed with classic trigeminal neuralgia was performed aimed to detect the Met136Val change. Results No cases of classical trigeminal neuralgia studied had the Met136Val mutation in SCN8A. Conclusion Met136Val mutation in SCN8A is not a frequent cause of classical trigeminal neuralgia., This paper provides evidence that the SCN8A Met136Val is not a common cause of trigeminal neuralgia.

Case control study was used,with Glanzmann’s thrombasthenia (GT) patients (n=15) and healthy individualcontrol (n=20).It was successfully identified three SNP in ITGB3 gene by using PCR technique and direct sequencing . Thefirst SNP c. * 1479T> C (rs115310198) was presented with three genotypes (TT, TC and CC). The genotypefrequencies of TT in control group (87.6 vs. 95 %) show non-significant difference (p>0.05) compared withGT patients . It was also noticed the frequency of mutant allele (C) revealed non-significant difference (p >0.05) in GT patients compared with controls group (13.3 vs. 2.5%; OR = 6; EF = 0.03; 95% C.I. = 0.65 to55.05) that mean (C) allele is risk factor associated with GT patients .The c.*713A>G (rs2317676) was given with three genotypes (AA, AG and GG) . The frequencies of thesegenotypes show non-significant difference (p>0.05) between control and GT patient,while the mutant allele(G) show non-significant difference (p > 0.05) in GT patients compared with controls group (16.6 vs. 5%;OR = 3.8; EF = 0.4; 95% C.I. = 0.70 to 20.63) and it was risk factors of patient GT. The c.*1016T>A(rs3809865) showed three genotypes (TT, TA and AA) with two alleles (T and A). The frequencies of thesegenotypes TT (87.6 vs. 85 %), TA (6.6vs. 15 %) and the third genotype AA (6.6 vs. 0%) show non-significantdifference (p>0.05) between control and GT patient but the genotype (AA) (OR= 4.24) was considered asrisk factors with GT patients . It was also found the mutant allele (A) revealed non-significant difference (p> 0.05) in GT patients compared with controls group (10 vs. 7.5%;OR = 1.37; EF = 0.11; 95% C.I. =0.26 to7.14). (A) allele(OR = 1.37) is positively associated with GT patients and negatively associated with healthysubject .

To date, there has been no reliable test to identify unfavorable course of Chronic Rhinosinusitis with Nasal Polyps (CRSwNP), especially in aspirin intolerant patients. The research aimed to analyze the expression of transcript variants of PTGS1 and PTGS2 genes in the pathobiology of the disease. The study was performed on 409 adult patients: 206 CRSwNP patients including 44 (21.36%) aspirin intolerant patients and 203 healthy volunteers in the control group. Transcript variants of the PTGS1 and PTGS2 genes named as follows: COX1.1 for NM_000962, COX1.2 for NM_080591, COX1.3 for NM_001271165.1, COX1.4 for NM_001271368.1, COX1.5 for NM_001271166.1, COX2.1 for NM_000963.3, COX2.2 for AY_151286 and COX2.3 for BQ_722004 were confirmed using direct sequencing and quantified using targeted qPCR. The coexistence of all examined transcript variants in the study and the control group and significant differences between both were found. In aspirin sensitive patients, the levels of COX1.2, COX1.3, COX1.4 and COX1.5 isoforms were higher compared to aspirin-tolerant patients. The severity of symptoms was bigger in patients with higher expressions of variants: COX1.1 (R with dCt = &minus, 0.134, p = 0.0490), COX1.3 (R = &minus, 0.1429, p = 0.0400) and COX1.5 (Rs = &minus, 0.1499, p = 0.032). The expression of COX1.1 (Rs = &minus, 0.098, p = 0.049) and COX1.5 (Rs = &minus, 0.141, p = 0.043) isoforms increased with polyposis advancement in endoscopy. With the CT extent of sinuses opacification, COX1.1 isoform also significantly increased (Rs = &minus, 0.163, p = 0.020). The isoforms COX1.3, COX1.4, COX1.5 and COX2.1 may promote milder CRSwNP course. On the contrary, the variants COX1.1, COX1.2 and COX2.2 may be involved in a more aggressive disease.

BackgroundIt is very rare for clear cell sarcomas (CCS) to arise in the bone. During diagnosis, it is important to distinguish primary CCS of bone from bone metastasis of melanoma because this difference fundamentally changes the therapeutic options. Recently, characteristic fusion genes of CCS have been detected using reverse transcription polymerase chain reaction (RT-PCR) or direct sequencing which allowed to distinguish CCS from melanoma. However, there was no study applying these analyses with positive results. In this case, we describe the use of fusion gene analysis to diagnose a primary CCS of the bone.Case presentationA 36-year-old male presented with a four-months history of left knee pain. Magnetic resonance imaging showed a lesion in the left femoral medial epicondyle. Histological examination of the biopsy specimen revealed proliferating oval or rounded cells. These cells had clear cytoplasm arranged in fascicles or compact nests with frequent deposits of brown pigment. Furthermore, immunohistochemistry analysis revealed that tumor cells were positive for S-100 protein, HMB-45, Melan-A, and SOX10. It stained negative for CD34 and BRAF v600e. Conclusively, detection of theEWSR1/ATF1fusion gene using RT-PCR and direct sequencing confirmed that the lesion was a primary CCS of the bone. Wide-margin resection and reconstruction with a tumor endoprosthesis were performed.ConclusionsHerein, we diagnosed a rare case of primary CCS of the bone by detectingEWSR1/ATF1fusion gene using RT-PCR and direct sequencing. Since fluorescence-in situ hybridization (FISH) and RT-PCR could show false positive by mainly due to technical problems, it is better to perform direct sequencing to confidently diagnose the tumor as a primary CCS especially at very rare site such as bone.

A statistically significant higher prevalence of the RET p.Met918Thr somatic mutation, identified by direct sequencing, was previously reported in MTC > 2 cm than in smaller tumors. Aim of this study was to correlate the full RET and RAS mutation profile, identified by a Next Generation Sequencing approach, with the growth rate, proliferation and tumor size of MTC. Data of 149 sporadic MTC patients were correlated with RET mutations and Ki67 positivity. Eighty-one cases had a somatic RET mutation, 40 had a RAS mutation and 28 were negative. A statistically significant higher prevalence of RET mutations was found in MTC > 2 cm. A higher prevalence of RET more aggressive mutations, higher allelic frequencies and, higher percentage of Ki67 positive cells were found in larger tumors which had also a worse outcome. Our study highlights the predominant role of RET somatic mutations in MTC tumorigenesis. We demonstrate that RET mutation prevalence and allelic frequency (AF) are significantly higher in larger tumors. Based on these results, we can conclude that RET mutated C-cells’s growth and proliferation are more rapid than those of non-mutated cells and give origin to bigger and more aggressive MTC.

Next-generation sequencing (NGS)’s crucial role in supporting genetic diagnosis and personalized medicine leads to the definition of Guidelines for Diagnostic NGS by the European Society of Human Genetics. Factors of different nature producing false-positive/negative NGS data together with the paucity of internationally accepted guidelines providing specified NGS quality metrics to be followed for diagnostics purpose made the Sanger validation of NGS variants still mandatory. We reported the analysis of three cases of discrepancy between NGS and Sanger sequencing in a cohort of 218 patients. NGS was performed by Illumina MiSeq® and Haloplex/SureSelect protocols targeting 97 or 57 or 10 gene panels usually applied for diagnostics. Variants called following guidelines suggested by the Broad Institute and identified according to MAF 0.2 were Sanger validated. Three out of 945 validated variants showed a discrepancy between NGS and Sanger. In all three cases, a deep evaluation of the discrepant gene variant results and methodological approach allowed to confirm the NGS datum. Allelic dropout (ADO) occurrence during polymerase chain or sequencing reaction was observed, mainly related to incorrect variant zygosity. Our study extends literature data in which almost 100% “high quality” NGS variants are confirmed by Sanger; moreover, it demonstrates that in case of discrepancy between a high-quality NGS variant and Sanger validation, NGS call should not be a priori assumed to represent the source of the error. Actually, difficulties (i.e., ADO, unpredictable presence of private variants on primer-binding regions) of the so-called gold standard direct sequencing should be considered especially in light of the constantly implemented and accurate high-throughput technologies. Our data along with literature raise a discussion on the opportunity to establish a standardized quality threshold by International Guidelines for clinical NGS in order to limit Sanger confirmation to borderline conditions of variant quality parameters and verification of correct gene variant call/patient coupling on a different blood sample aliquot.

The pharmacokinetics of CYP2C9 substrates is characterized by substantial interethnic variability. The objective of the study was to compare CYP2C9 activity by using Phenytoin Metabolic Ratio (PMR) between Ethiopian and non-Ethiopian Jews. PMR was derived from the ratio of p-HPPH in 24-hours urine collection to plasma phenytoin, 12 hours (PMR24/12) or 24 hours (PMR24/24) after the administration of 300 mg phenytoin. Analysis of CYP2C9*2, *3, *5, *6, *8 and *11 was carried by direct sequencing. PMR was significantly correlated with CYP2C9 genotype in both groups (p< 0.002). Mean PMR values were similar among Ethiopians and non-Ethiopians despite the fact that the fraction of non-carriers of CYP2C9 variant alleles was significantly different (85% vs. 53%, respectively, p< 0.001). However, among non-carriers of CYP2C9*2, *3, *5, *6, *8 and *11 variant alleles, PMR24/12 and PMR24/24 values were 30% and 34% greater respectively in the non-Ethiopians group (p< 0.001). In conclusion – CYP2C9 activity as measured by PMR is similar in Ethiopian and non-Ethiopian Jews. However, among non-carriers of CYP2C9 variant alleles accounting for 85% of Ethiopian Jews, CYP2C9 activity is decreased by approximately one third as compared with non-Ethiopian Jews. Unique genetic CYP2C9 polymorphisms occurring only in Ethiopians may account for this difference.

Background In recent years, several high‐risk human papillomavirus (HR‐HPV) tests have been developed. The assay capabilities need to be systematically reviewed. Here, we compared the clinical sample performance of three novel HR‐HPV assays (Liferiver, Yaneng, and Darui) based on different platforms with the widely adopted cobas4800 test. Methods A total of 346 cervical swabs from women who were screened for cervical cancer were analyzed for the presence of 14 HR‐HPV genotypes. The distinction between the four assays was investigated by the genotyping and direct sequencing. Results The positive rates of the four assays ranged from 61.56% to 64.16%. The overall concordance was 88.15%. The Yaneng assays displayed the best sensitivity (100%) and specificity (98.43%). The sensitivity (98.17%) and specificity (98.43%) of the Darui assay were superior to those of the cobas4800 test (97.72% and 93.70%, respectively). The Liferiver assay displayed comparable sensitivity with the cobas4800 test (95.89% and 97.72%, respectively). The specificity of the cobas4800 was lower than that of the Liferiver assay (93.70% vs. 97.64%). Conclusions The three novel HR‐HPV assays displayed good agreement with the cobas4800 test. The analytical performance of all four fulfilled the requirements of sensitivity and specificity for HR‐HPV detection., In this research, we have compared the clinical sample performance of three novel HR‐HPV assays (Liferiver, Yaneng, and Darui) based on different platforms with the widely adopted cobas4800 test, and the distinction between the four assays was investigated by the genotyping and direct sequencing.

Background Ectodermal dysplasias are a group of genodermatoses characterized by dystrophy of ectodermal derived structures. The most frequent presentation of the ectodermal dysplasias is the hypohidrotic type, which has an incidence of 7/100,000 newborns and has been described in all ethnic groups. The hypohidrotic ectodermal dysplasia (HED) has different etiologies, and it is more frequently associated with an X-linked pattern of inheritance caused by pathogenic variants of the EDA gene in Xq13.1. EDA encodes the protein ectodisplasin A, a signal molecule which participates in epithelium and mesenchymal development of the skin. Case report A 6 year-old male patient with the main clinical characteristics of the X-linked HED including hypotrichosis, hypodontia and hypohidrosis. The direct sequencing analysis of EDA in our patient detected a de novo pathogenic variant, c.466C>T, p.Arg156Cys, rs132630313. This variant has been previously described in different ethnic groups, including Mexican families, and is considered a mutational hotspot. The clinical characteristics, etiology and management of the X-linked HED, including the possibility of prenatal therapy in order to avoid the clinical manifestations are discussed. Conclusions The molecular analysis in patients with X-linked HED is of relevance, as it enables to confirm the clinical diagnosis and also, it allows a genetic assessment with molecular bases.

Betapapillomaviruses have been linked to the development of nonmelanoma skin cancers. A great diversity of these viruses in skin specimens requires the use of sensitive and reliable detection methods. There are currently no standardized assays for diagnostic purposes. A combination of several molecular methods has great practical significance and gives the opportunity to broaden the spectrum of detected Beta-HPV types. In the present study, different molecular methods for Beta-HPVs detection and genotyping were used: PCRs with different sets of primers, PCR followed by reverse hybridization and direct sequencing of PCR amplimers; all performed in skin biopsies from lesions and perilesional healthy area of 118 patients with NMSC or precancerous lesions. Beta-HPVs were detected in 41% of 261 biopsies examined. The RHA for 25 types of Beta-HPVs showed a significantly higher sensitivity than PCR-based methods and allowed to detect 172 genotypes in 86 samples, including 39 with multiple infections. The most frequently identified types were HPV23, HPV24 and HPV93. HPV5 and HPV8, considered high-risk carcinogen types, were detected only in a small percentage of samples. Direct sequencing confirmed the presence of Beta-HPV genotypes from outside of RHA panel in the analysed biopsies. This allowed detecting thirty-two additional genotypes in 5 samples, that were positive only in RHA with the universal probe, which failed to identify the virus genotypes. Our findings confirmed the need to apply different methods to detect Beta-HPV infections.

Hereditary coagulation factor XI (FXI) deficiency is a rare bleeding disorder, but information on FXI deficiency in Taiwanese patients remains scarce. We evaluated clinical and genetic features of severe FXI deficiency patients in Taiwan. We collected clinical information and performed coagulation laboratory tests and genetic studies in ten unrelated Taiwanese families with severe FXI deficiency. FXI coagulation activity was assayed using a one-stage method. FXI antigen was determined using enzyme-linked immunosorbent assay. Underlying genetic mutations were evaluated using direct sequencing methods. Ten unrelated Taiwanese patients with hereditary FXI deficiency and variable bleeding tendencies were analyzed. Half of the patients were male. The most common bleeding manifestations were easy bruising (40%), bleeding after dental procedures (40%), and postoperative bleeding (33%). Two patients (20%) were asymptomatic. No correlation was found between bleeding manifestations and baseline FXI levels. Three novel mutations were identified: c.1322delT p.Lys442Cysfs*8, c.599G > C p.Cys200Ser, and IVS4 c.325 + 2del124. Two common mutations, c.1107C > T p.Tyr369* (40%) and c.841C > T p.Gln281* (30%), were also found. No correlation existed between bleeding and FXI activity, highlighting the difficulty in predicting FXI deficiency-related bleeding. Three novel FXI genetic mutations and two common mutations were identified, contributing to the known spectrum of FXI deficiency-related mutations.

Hepatitis B with precore stop codon mutation is related with severe liver damage in HBeAg negative patients. It is of utmost importance to screen the G1896A precore mutation. The study was designed to assess the impact of G1986A mutations in patients with different clinical spectra of the liver disease by PCR–LCR. 210 HBV positive patients with HBeAg negative serology of different kind of liver diseases (AVH = 72, FH = 21, CH = 79, Cirrhosis = 20 and HCC = 18) were screened. Patients were screened for the presence or absence of precore G1896A mutation by PCR–LCR. Direct nucleotide sequencing was done to confirm the results of LCR. Precore mutant in HCC was 94.4% (17/18), 85.7% (18/21) in FH, 60% (12/20) in liver cirrhosis, 48.1% (38/79) in chronic hepatitis and 27.7% (20/72) in AVH cases. The serum ALT level was statistically significant between HBeAg negative WT and G1896A mutants in chronic hepatitis cases. ALT level and HBV DNA level was slightly raised in the pre core mutant but and was not significant. Genotype D had a higher prevalence (79.5%) as compared to genotype A (20.5%). The mutations detected by PCR–LCR were in 100% concordance with direct sequencing. The exceptionally high prevalence of G1896A in FH and HCC demonstrates that the precore mutants are strongly associated with the progression of liver diseases in patients with HBeAg negative serology. The findings are also suggestive of screening HBV precore G1896A mutation particularly in HBeAg negative cases. The precore G1896A mutation increases proportionately in severe form of liver diseases. LCR can be a suitable tool for screening of G1896A mutations. Keywords: Hepatitis B, G1896A, Mutation, Ligase chain reaction, Direct sequencing, Serology

BackgroundKawasaki disease is the leading cause of acquired heart disease in children from developed countries. The Interleukin-6/ Interleukin-12 cytokine family has many members, including the paradoxical anti- and pro-inflammatory Interleukin-27. Recent studies have demonstrated that Interleukin-27 plays a role in immune diseases. Given this, we sought to evaluate the association betweenInterleukin-27genetic polymorphisms and Kawasaki disease in Chinese children.Methods and resultsInterleukin-27 was genotyped in 100 Kawasaki disease children and 98 healthy children (controls), resulting in the direct sequencing of eight Single-nucleotide Polymorphisms: rs17855750, rs40837, rs26528, rs428253, rs4740, rs4905, rs153109, and rs181206). There were no significant differences in Interleukin-27 genotypes between Kawasaki disease and control groups. Of the eight Single-nucleotide Polymorphisms, there was a significant increase in the risk of Kawasaki disease with coronary arterial lesions in children with the rs17855750 (T>G), rs40837 (A>G), rs4740 (G>A), rs4905 (A>G), rs153109 (T>C), and rs26528 (A>G) Single-nucleotide Polymorphisms. This was particularly true for rs17855750 (T>G), which had a greater frequency in Kawasaki disease children with coronary arterial aneurysm.ConclusionThese findings may be used as risk factors when assessing a child’s likelihood of developing Kawasaki disease, as well as for the development of future therapeutic treatments for Kawasaki disease.

The aim of the study was to establish the clinical and laboratory features of Lyme borreliosis (LB) and borreliosis caused by Borrelia miyamotoi in adults from Novosibirsk region. Materials and methods. The study included 724 patients, residents of the Novosibirsk region, hospitalized with a fever that arose after a tick bite in the epidemic seasons 2015–2017. In all patients, clinical manifestations of the disease, hemogram parameters and biochemical parameters of blood serum were studied. DNA of B. miyamotoi was detected in blood and cerebrospinal fluid (CSF) of patients using nested PCR; the results were confirmed by direct sequencing of PCR fragments. LB was diagnosed by the presence of erythema migrans as well as by the detection of Borrelia burgdorferi sensu lato DNA by PCR and/or specific IgM by ELISA. Results and discussion. B. miyamotoi DNA of the Asian type was identified in samples from 10,2% of 724 examined patients, LB with erythema migrans was diagnosed in 16,0% of patients, and LB without erythema migrans was revealed in 4,6% of patients. All patients with B. miyamotoi infection had high or moderate fever and symptoms of intoxication in the absence of erythema migrans; 13,5% of patients with B. miyamotoi had meningeal symptoms without any changes in the CSF. Notably, the changes in leukocyte formula were recorded more often in patients with B. miyamotoi compared to those with LB (p

PURPOSE This study aimed to evaluate the performance of the PANArray human papilloma virus (HPV) test, a PCR-based DNA microarray assay, in detecting HPV from patient samples and its concordance with the cobas 4800 HPV and Hybrid Capture 2 (HC2) tests. MATERIALS AND METHODS The PANArray HPV, cobas 4800 HPV, and HC2 tests were performed on 504 cervical swab samples from patients with atypical cells of undetermined significance at five hospitals. The samples that were interpreted as 'HPV-other' type positive in the PANArray HPV test were confirmed by direct sequencing. RESULTS The concordance rates were 80.8% between the cobas 4800 HPV and PANArray HPV tests [κ=0.59, 95% confidence interval (CI) 0.52-0.66] and 80.2% (κ=0.6, 95% CI 0.55-0.68) between the HC2 and PANArray HPV tests. Among the 62 patients negative on PANArray HPV (defined as the absence of high risk HPV), but positive on both cobas 4800 HPV and HC2 tests, 42 (67.7%) tested positive for 'HPV-other' types on the PANArray HPV test, and 31 (50.0%) had gray zone results [relative light unit/control (RLU/CO), 1.4-9.25] in the HC2 test. Of the patients deemed positive by the PANArray HPV test, 43 tested positive for high-risk (HR) HPV in cobas 4800 HPV and HC 2 tests. Among them, 58.2% showed HR HPV, including HPV 16, by direct sequencing, of which 25% had gray results. CONCLUSION Results classified as 'HPV-other' type by the PANArray HPV test, or gray zone results by HC2 (RLU/CO ratio level 1-10) should be carefully interpreted using comprehensive clinical information.

Aim of the study To describe a family with primary familial brain calcification (PFBC) due to SLC20A2 variant showing possible genetic anticipation. Materials and methods We conducted historical, genealogical, clinical, and radiologic studies of a family with PFBC. Clinical evaluations including neurological examination and head computed tomography (CT) scans of a proband and her father were performed. They provided additional information regarding other family members. To identify a causative gene variant, we performed whole-exome sequencing for the proband followed by segregation analysis in other affected members using direct sequencing. Results In this family, nine affected members were identified over four generations. The proband suffered from chronic daily headache including thunderclap headache. We identified an SLC20A2 (c.509delT, p.(Leu170*)) variant in three affected members over three generations. Interestingly, the age of onset became younger as the disease passed through successive generations, suggestive of genetic anticipation. Conclusions and clinical implications For clinical purpose, it is important to consider thunderclap headache and genetic anticipation in PFBC caused by SLC20A2 variants. Further investigation is required to validate our observation.

Branchio-oto-renal (BOR) syndrome is a rare autosomal dominant disorder characterized by branchial cleft fistulae or cysts, preauricular pits, ear malformations, hearing loss, and renal anomalies. Mutations in the human homologue of the Drosophila eyes absent gene (EYA1) are the most common cause of BOR syndrome. PCR and direct sequencing were used to investigate all of the exons and exon-intron boundaries in the EYA1 gene in a patient with BOR syndrome from China. The patient was a child who displayed clinical features of BOR syndrome. Analysis of mutations in the EYA1 gene revealed a novel single base-pair deletion resulting in a truncated protein (c.1381delA; p.R461fs467X), and an analysis of mutations in the family revealed that this mutation was a de novo mutation. This is the first case of BOR syndrome in mainland China to be diagnosed based on clinical manifestations and mutations in the EYA1 gene. The novel c.1381delA mutation detected here expands the spectrum of known mutations in the EYA1 gene.

A 41-year-old woman presented with recurrent dizziness. After an attack of dizziness, she felt edematous sensations in her hands. However, according to photographs taken during the attack, the edema on the back of the patient’s hands and fingers appeared mild. Laboratory examinations revealed a low C4 and C1 inhibitor (INH) activity. A direct sequencing analysis of C1INH revealed a pathogenic gene mutation. Based on these results, she was diagnosed with hereditary angioedema (HAE) type 1. These findings indicate that HAE can cause recurrent dizziness, and it should therefore be included in the differential diagnosis in patients with recurrent neurologic symptoms, even in the absence of severe edema.

Gas station workers are exposed to chemicals known to be carcinogenic, especially benzene. The objective was to analyze the health problems of female gas station workers by means of sociodemographic and clinical questionnaires, and laboratorial exams. We performed the genotyping of the polymorphisms BRCA1/P871L and BRCA1/Q356R by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism, and of variant allele BRCA2/N372H through direct sequencing. The female workers showed a higher concentration of monocytes (P = 0.039); a greater number of spontaneous abortions (P = 0.025, OR = 4.977, 95% CI = 1.135-30.669); higher tobacco consumption (P = 0.013); and higher alcohol consumption (P = 0.05). The statistical analysis of the polymorphisms associated with the variables monocyte concentration and miscarriage number did not reveal a significant relationship, and smoking and spontaneous abortion were not statistically associated either. Environ. Mol. Mutagen. 58:730-734, 2017. © 2017 Wiley Periodicals, Inc.

Objective The study was accompanied to evaluate the specificity, cost and turn-around time of three different types of techniques that can be used for analysis of single nucleotide polymorphism of rs129796860. Methods One hundred and one samples of patients infected with chronic Hepatitis C were genotyped with the three types of genotyping methods: direct sequencing, SNaPshot PCR and PCR-Restriction fragment Length polymorphism. Results Three distinct profiles for IL28B rs12979860 alleles (CC, CT and TT) were obtained with direct sequencing; SNaPshot PCR and PCR-RFLP and the results were consistent among the three methods. Conclusion Hence, it could be suggested that for routine medical practice screening of IL28B rs12979860 could be done by PCR-Restriction fragment Length polymorphism that is the efficient and reliable as well as cost effective method. Copyright © 2017 John Wiley & Sons, Ltd.

// Qi Feng 1,* , Zu-Yao Yang 1,* , Jia-Tong Zhang 1 and Jin-Ling Tang 1 1 Division of Epidemiology, JC School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong * These authors have contributed equally to this work Correspondence to: Jin-Ling Tang, email: // Keywords : epidermal growth factor receptor, direct sequencing, amplification refractory mutation system, non-small cell lung cancer, tyrosine kinase inhibitors Received : January 17, 2017 Accepted : June 27, 2017 Published : July 08, 2017 Abstract Background: Direct sequencing and amplification refractory mutation system (ARMS) are commonly used to detect epidermal growth factor receptor ( EGFR ) mutation status in patients with non-small-cell lung cancer to inform the decision-making on tyrosine kinase inhibitors treatment. This study aimed to systematically compare the two methods in terms of the rate of detected mutations and the association of detected mutations with clinical outcomes. Material and methods: PubMed, EMBASE, China National Knowledge Infrastructure (in Chinese) and Wanfang database (in Chinese) were searched to identify relevant studies. Meta-analyses of EGFR mutation rates, rate differences, and the associations of EGFR mutations with clinical outcomes of tyrosine kinase inhibitors treatment were conducted. Results: Eight hundred and sixty-six records were retrieved and 26 studies with 3282 patients were included. The pooled rate of mutations detected by ARMS (41%, 95% confidence interval (CI) 35% to 47%) was significantly higher than that by direct sequencing (28%, 95%CI 22% to 34%), with a weighted rate difference of 11% (95%CI 8% to 13%). There was a consistent trend that the associations between ARMS-detected mutations and clinical outcomes were stronger than those between direct-sequencing-detected mutations and clinical outcomes (pooled risk ratio for objective response: 5.18 vs . 2.25; hazard ratio for progression-free survival: 0.30 vs . 0.42; hazard ratio for overall survival: 0.46 vs . 0.54). Conclusions: More patients with EGFR mutations can be identified by ARMS than by direct sequencing, and those identified by ARMS seems to be able to benefit more from tyrosine kinase inhibitors than those identified by direct sequencing.

Background: This report describes a 45-year-old man with complete congenital stationary night blindness (CSNB1) who has been followed up for 38 years. Case: The patient first visited our hospital as a 7-year-old boy with a complaint of low visual acuity. Best corrected visual acuity (BCVA) was 0.5 in the right eye and 0.6 in the left eye. The refractive error was approximately –5.0 D in both eyes. The fundus showed only myopic changes. A bright-flash electroretinogram (ERG) revealed a negative configuration. We diagnosed CSNB and corrected the refractive error with glasses. We continued to monitor the ERG and various waveform components as well as visual acuity and the appearance of the fundus. All NYX exons were screened for a causative mutation by polymerase chain reaction amplification, and direct sequencing was performed. Results: By 10 years of age, BCVA had increased to 0.8 on the right and 0.9 on the left, with little change thereafter. The fundus continued to show only myopic changes. No changes were seen in the amplitude or implicit time of the a-wave or b-wave or in the b/a-wave ratio. A novel hemizygous insertion mutation, c.1205_1206insT, p.(Glu404Argfs*89), was detected in exon 2 of the NYX gene. Conclusion: To our knowledge, this is the longest follow-up of a patient with CSNB1. No changes in the clinical course have been seen during follow-up. We believe that it is important to continue observations and accumulate clinical data for prognostic purposes on patients with CSNB1.

Key Clinical Message In selected cases, homozygosity mapping followed by direct sequencing of one or a few carefully selected candidate genes in a prenatal setting can be beneficial to obtain diagnosis in consanguineous families.

Dried scallop adductor muscle, known as yao zhu, has been ranked in the list of the eight sea treasures in Chinese cuisine, it has been commonly recommended and consumed in China over many centuries due to its delicious taste and abundant nutrition. However, the true species composition of the dried scallop adductor muscles in the trade is unclear. Indeed, it is difficult to identify the scallop species just based on their morphological characters of processed adductor muscles. In this study, 60 yao zhu products commercialized in Chinese market were analyzed in order to authenticate species. Direct sequencing and BLAST method based on a fragment of the 16S rRNA gene were carried out and results showed that 34 products (56.7%) were scallop species Argopecten irradians, and other 26 products (43.3%) were the scallop species Mizuhopecten yessoensis, indicated the yao zhu market were dominated by the both species, which were the introduced aquaculture scallop species. Moreover, a simple and fast PCR method proved to be capable of unequivocal identification between the two species. Therefore, this work facilitates the identification of yao zhu products in the market, support of food control and protection of consumers’ rights.

В работе представлены результаты расширенного генетического исследования 39 детей, наблюдавшихся в КДЦ «Охрана здоровья матери и ребенка» (г. Екатеринбург) с диагнозом «гиперфенилаланинемия». Анализ результатов обследования детей (у 13-ти пробандов наличие варианта R408W в гетерозиготном состоянии) показал, что поиск рекуррентных вариантов гена с использованием панели для ДНК-диагностики не дает ожидаемой верификации диагноза и требует дополнительного тестирования. Прямое секвенирование гена PAH позволило подтвердить диагноз «фенилкетонурия» (ФКУ) у 35 пробандов (89,8%) - у них обнаружено по 2 измененных аллеля. Еще у 4-х пациентов обнаружен только один патогенный вариант. Исследование ДНК родителей и сибсов указало на семейный вариант наследования всех выявленных мутаций. В результате проведенного исследования спектр патологии гена PAH, характерный для популяции Свердловской области, претерпел существенные изменения, что требует нового подхода к генодиагностике данной наследственной патологии в регионе. The paper presents the results of an extended genetic study of 39 children observed in the MC “Health Care of Mother and Child” (Ekaterinburg) with a «hyperphenylalaninemia». An analysis of the previously known results of the study in these patients (the p. R408W variant in the heterozygous in 13 probands) showed that the search for recurrent gene variants using the panel does not give the expected proving of the diagnosis and requires additional testing. Applying the «gold standard» of diagnosis - direct sequencing of the PAH gene, the diagnosis of phenylketonuria (PKU) was confirmed in 35 probands (89.8%) - 2 altered alleles were found in them, one pathogenic variant was found in 4 others. A study of the DNA of parents and siblings indicated a families’ variants of inheritance for all identified mutations. As a result of the study, the pathology spectrum of the PAH gene, currently in use for the population of the Sverdlovsk region, has undergone significant changes, which require a new approach to the genetic diagnosis of this hereditary pathology in the region.