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Introduction: The classic Philadelphia chromosome–negative myeloproliferative neoplasms (Ph (‐) MPNs), have variable potential for progression to the blast phase (MPN‐BP) of the disease. Except initiated by distinct driver mutations, MPN‐BP frequently carry similar genetic abnormalities defining acute myeloid leukemia myelodysplasia‐related (AML‐MR). Because of dissimilar initial pathogenesis, MPN‐BP and AML‐MR are retained under different disease categories. To determine if separately classifying these entities is justified, we compare MPN‐BP with AML‐MR patients based on mutational landscape and clinical parameters. Methods: 104 MPN‐BP patients and 145 AML‐MR patients were identified with available clinical, cytogenetic, and genetic data. Results: AML‐MR patients presented with a higher blast count (median, 51% vs. 30%) while MPN‐BP patients had higher WBC counts, platelet counts and bone marrow cellularity (all p<0.0001). Patients with MPN‐BP showed similar genetic mutations with similar mutation pattern (functional domain, hotspot and locus involved by the mutations) but a different mutation rate from AML‐MR, with more frequent JAK2, CALR, MPL, ASXL1, IDH2, SETBP1 and SRSF2 mutations and less frequent TP53 and DNMT3A mutations. The overall survival (OS) of MPN‐BP (OS post‐BP‐progression) is comparable to that of AML‐MR (median OS, 9.5 months vs. 13.1 months, p=0.20). In addition, the subgroups of MPN‐BP show similar OS as AML‐MR. When harboring certain mutation such as TP53, ASXL1, DNMT3A, TET2, RUNX1, IDH1, IDH2, EZH2, U2AF1, BCOR and SRSF2, MPN‐BP and AML‐MR patients carrying the same somatic mutation show no difference in OS. Conclusion: MPN‐BP and AML‐MR harbor similar somatic mutations and clinical outcomes, suggesting a unified clinical disease entity. [ABSTRACT FROM AUTHOR]

The blast phase of BCR::ABL1‐negative myeloproliferative neoplasm (MPN‐BP) represents the final stage of the disease, which is complicated by complex genomic alterations. These alterations result from sequence changes in genetic material (DNA, RNA) and can lead to either a gain or loss of function of encoded proteins, such as adaptor proteins, enzymes, components of spliceosomes, cell cycle checkpoints regulators, transcription factors, or proteins in cell signaling pathways. Interference at various levels, including transcription, translation, and post‐translational modification (such as methylation, dephosphorylation, or acetylation), can contribute to these alterations. Mutated genes such as ASXL1, EZH2, IDH1, IDH2, TET2, SRSF2, U2AF1, TP53, NRAS, KRAS, PTPN11, SH2B3/LNK, and RUNX1 play active roles at different stages of genetic material expression, modification, and protein function manipulation in MPNs. These mutations are also correlated with, and can contribute to, the progression of MPN‐BP. In this review, we summarize their common mutational profiles, functions, and associations with progression of MPN‐BP. [ABSTRACT FROM AUTHOR]

Revised diagnostic criteria for myeloid neoplasms (MN) issued by the International Consensus Classification (ICC) and the World Health Organization (WHO) recommended major change pertaining to TP53-mutated (TP53mut) MN. However, these assertions have not been specifically examined in therapy-related myeloid neoplasm (t-MN), a subset enriched with TP53mut. We analyzed 488 t-MN patients for TP53mut. At least one TP53mut with variant allele frequency (VAF) ≥ 2% with or without loss of TP53 locus was noted in 182 (37.3%) patients and 88.2% of TP53mut t-MN had a VAF ≥10%. TP53mut t-MN with VAF ≥ 10% had a distinct clinical and biological profile compared to both TP53mut VAF < 10% and wild-type TP53 (TP53wt) cases. Notably, TP53mut VAF ≥ 10% had a significantly shorter survival compared to TP53wt (8.3 vs. 21.6 months; P < 0.001), while the survival of TP53mut VAF < 10% was comparable to TP53wt. Within TP53mut VAF ≥ 10% cohort, the inferior outcomes persisted irrespective of the single- or multi-hit status, co-mutation pattern, or treatments received. Finally, survival of TP53mut patients was poor across all the blast categories and MDS patients with >10% blasts had inferior survival compared to <5%. In summary, TP53mut VAF ≥10% signified a clinically and molecularly homogenous cohort regardless of the allelic status. [ABSTRACT FROM AUTHOR]

Objectives: KDF1 is a recently identified gene related to tooth development, but it has been little studied. To date, only three cases have been reported in which KDF1 mutations are related to tooth development, including two ectodermal dysplasia cases accompanied by tooth loss and one non-syndromic case with tooth agenesis. However, no KDF1 mutations have been reported as associated with non-syndromic anodontia. Here, the aim was to investigate the genetic etiology of this condition and explore the functional role of a novel KDF1 mutation in a Chinese patient with non-syndromic anodontia. Materials and methods: Pathogenic variants were identified by whole-exome and Sanger sequencing. Meanwhile, we conducted a literature review of the reported KDF1 mutations and performed an in vitro functional analysis of four anodontia-causing KDF1 mutations (one novel and three known). Results: We identified a novel de novo missense mutation (c.911 T > A, p.I304N) in the KDF1 gene in a Chinese patient with severe non-syndromic anodontia. In vitro functional studies showed altered mRNA and protein expression levels of the mutant KDF1. Conclusions: Our results are the first report of KDF1 missense mutation causing non-syndromic anodontia. Clinical relevance: This study not only further supports the important role of KDF1 in non-syndromic congenital anodontia, but also expands the spectrum of KDF1 mutations and will contribute to the genetic diagnosis and counselling of families with anodontia. [ABSTRACT FROM AUTHOR]

DNMT3A mutations play a prominent role in clonal hematopoiesis and myeloid neoplasms with arginine (R)882 as a hotspot, however the clinical implications of R882 vs. non-R882 mutations in myeloid neoplasms like myelodysplastic syndrome (MDS) is unclear. By data mining with publicly accessible cancer genomics databases and a clinical genomic database from a tertiary medical institution, DNMT3A R882 mutations were found to be enriched in AML (53% of all DNMT3A mutations) but decreased in frequency in clonal hematopoiesis of indeterminate potential (CHIP) (10.6%) or other myeloid neoplasms including MDS (27%) (p<.001). Next with the largest cohort of patients with DNMT3A R882 mutant MDS known to date from multiple institutions, DNMT3A R882 mutant MDS cases were shown to have more severe leukopenia, enriched SRSF2 and IDH2 mutations, increased cases with excess blasts (47% vs 22.5%, p=.004), markedly increased risk of AML transformation (25.8%, vs. 1.7%, p=.0001) and a worse progression-free survival (PFS) (median 20.3, vs. >50 months, p=.009) than non-R882 mutant MDS cases. DNMT3A R882 mutation is an independent risk factor for worse PFS, and importantly the differences in the risk of AML transformation between R882 vs. non-R882 mutant patients cannot be explained by different treatment approaches. Interestingly the higher risk of AML transformation and the worse PFS in DNMT3A R882 mutant MDS cases are mitigated by coexisting SF3B1 or SRSF2 mutations. The unique clinicopathologic features of DNMT3A R882 mutant MDS shed light on the prognostic and therapeutic implications of DNMT3A R882 mutations. [ABSTRACT FROM AUTHOR]

Background: Colorectal neuroendocrine carcinomas (CRNECs) are highly aggressive tumours with poor prognosis and low incidence. To date, the genomic landscape and molecular pathway alterations have not been elucidated.Methods: Tissue sections and clinical information of CRNEC (n = 35) and CR neuroendocrine tumours (CRNETs) (n = 25) were collected as an in-house cohort (2010-2020). Comprehensive genomic and expression panels (AmoyDx® Master Panel) were applied to identify the genomic and genetic alterations of CRNEC. Through the depiction of the genomic landscape and transcriptome profile, we compared the difference between CRNEC and CRNET. Reverse transcription-polymerase chain reaction and immunofluorescence staining were performed to confirm the genetic alterations.Results: High tumour mutation load was observed in CRNEC compared with CRNET. CRNECs showed a "cold" immune landscape and increased endothelial cell activity compared with NETs. Importantly, PAX5 was aberrantly expressed in CRNEC and predicted a poor prognosis of CRNECs. CCL5, a factor that is considered an immunosuppressive factor in several tumour types, was strongly expressed in CRNEC patients with long-term survival and correlated with high CD8+ T cell infiltration.Conclusion: Through the depiction of the genomic landscape and transcriptome profile, we demonstrated alterations in molecular pathways and potential targets for immunotherapy in CRNEC. [ABSTRACT FROM AUTHOR]

Philadelphia (BCR‐ABL)‐negative myeloproliferative neoplasms (MPNs) include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). MPN can transform into an accelerated or a blast phase, which is associated with poor response to standard therapy and low overall median survival. We present an interesting case of a patient with a history of PMF and progression and summarize the current studies on genetic features of myeloproliferative neoplasms in blast phase (MPN‐BP) with an emphasis on PMF. Although MPN‐BP show ≥20% blasts in peripheral blood or bone marrow, it is not considered as acute myeloid leukemia (AML) according to the WHO classification. While MPNs‐BP typically lack genetic mutations seen in de novo AML, they commonly harbor IDH1/2, SRSF2, ASXL1, and TP53 mutations, similar to the genetic profiles of acute myeloid leukemia with myelodysplasia‐related changes (AML‐MRC). [ABSTRACT FROM AUTHOR]

Background: Degenerative lumbar spinal stenosis (DLSS) is a common lumbar disease that requires surgery. Previous studies have indicated that genetic mutations are implicated in DLSS. However, studies on specific gene mutations are scarce. Whole-exome sequencing (WES) is a valuable research tool that identifies disease-causing genes and could become an effective strategy to investigate DLSS pathogenesis. Methods: From January 2016 to December 2017, we recruited 50 unrelated patients with symptoms consistent with DLSS and 25 unrelated healthy controls. We conducted WES and exome data analysis to identify susceptible genes. Allele mutations firstly identified potential DLSS variants in controls to the patients' group. We conducted a site-based association analysis to identify pathogenic variants using PolyPhen2, SIFT, Mutation Taster, Combined Annotation Dependent Depletion, and Phenolyzer algorithms. Potential variants were further confirmed using manual curation and validated using Sanger sequencing. Results: In this cohort, the major classification variant was missense_mutation, the major variant type was single nucleotide polymorphism (SNP), and the major single nucleotide variation was C > T. Multiple SNPs in 34 genes were identified when filtered allele mutations in controls to retain only patient mutations. Pathway enrichment analyses revealed that mutated genes were mainly enriched for immune response-related signaling pathways. Using the Novegene database, site-based associations revealed several novel variants, including HLA-DRB1, PARK2, ACTR8, AOAH, BCORL1, MKRN2, NRG4, NUP205 genes, etc., were DLSS related. Conclusions: Our study revealed that deleterious mutations in several genes might contribute to DLSS etiology. By screening and confirming susceptibility genes using WES, we provided more information on disease pathogenesis. Further WES studies incorporating larger DLSS patient cohorts are required to comprehend the genetic landscape of DLSS pathophysiology fully. [ABSTRACT FROM AUTHOR]

Summary: Compound epidermal growth factor receptor (EGFR) mutations are defined as double or multiple independent mutations of the EGFR tyrosine kinase domain (TKD), in which an EGFR-tyrosine kinase inhibitor (TKI)-sensitizing mutation is identified together with a mutation of unclarified clinical significance. Lung adenocarcinoma with compound EGFR mutation shows poor clinical response to EGFR-TKIs. Kobayashi et al. reported a non-small-cell lung cancer (NSCLC) patient whose tumor had EGFR exon21 L858R/A871G mutation presented rapid disease progression to erlotinib. However, in this case, we present an EGFR exon21 L858R/A871G mutation patient exerted significant benefit to icotinib, another first-generation EGFR-TKI, indicating that different EGFR-TKIs have diversiform sensitive sites and therapeutic effects, consistent mutation sites might achieve heterogeneous benefits from different EGFR-TKIs. Our case report provides promising EGFR-TKI for clinical treatment with EGFR exon21 L858R/A871G mutation in NSCLC. More dedicated efforts are needed to clarify their biologic effects on disease course and drug responsiveness. [ABSTRACT FROM AUTHOR]

• A 39-year-old man presents to ALS clinic with progressive symmetric distal weakness. • Genetic studies find 2 novel variants in the SIGMAR1 gene. • The SIGMAR1 gene has been associated with a distal hereditary motor (dHMN). • Unlike ALS, dHMN has a symmetric distal pattern and more indolent disease course. • dHMN is a more accurate name for SIGMAR1- related disease than juvenile ALS. Distal hereditary motor neuropathy (dHMN) is an inherited neuromuscular disease characterized by symmetric distal weakness and atrophy without sensory changes. There are about thirty known genes associated with dHMN, but together they explain only about a third of cases. Mutations in the sigma non-opioid intracellular receptor 1 gene (SIGMAR1) has been linked to autosomal recessive dHMN with pyramidal signs in several families. This phenotype can mimic amyotrophic lateral sclerosis (ALS). We report a 39-year-old man who was referred to our ALS clinic with distal motor weakness and hyperreflexia. Whole exome sequencing identified two novel variants in the SIGMAR1 gene in the proband. Targeted Sanger sequencing of asymptomatic family members confirmed that each carried one of these two variants. Our findings expand the number of known SIGMAR1 pathogenic variants associated with dHMN, which should be clinically distinguished from ALS. [ABSTRACT FROM AUTHOR]

Patients with a sole del(20q) chromosomal abnormality and without morphologic features of a myeloid neoplasm (MN) have shown variable clinical outcomes. To explore the potential risk stratification markers in this group of patients, we evaluated their genetic mutational landscape by a 35-gene MN-focused next-generation sequencing (NGS) panel and examined the association of mutations to progression of MNs. Our study included 56 patients over a 10-year period with isolated del(20q), of whom 23 (41.1%) harbored at least one mutation. With a median follow-up of 32.6 months (range: 0.1−159.1), 9 of 23 patients with mutation(s) progressed to MNs, while all 33 patients without mutations did not progress to MN. Kaplan−Meier survival analysis demonstrated the presence of mutation(s) as a significant risk factor for progression to MN (P < 0.0001). MN progression was strongly associated with the presence of non-DNMT3A/TET2/ASXL1 epigenetic modifiers and nonspliceosome mutations (P = 0.003). There was no significant difference among patients with and without MN progression with respect to the number of mutations, variant allele frequency, percentage of del(20q), and other clinical/laboratory variables. This study illustrates the underlying genetic heterogeneity and complexity of isolated del(20q), and underscores the prognostic value of NGS mutational analysis in these cases. [ABSTRACT FROM AUTHOR]

Introduction: Mutations in gap junction protein beta 1 (GJB1) on the X chromosome represent one of the most common causes of hereditary neuropathy. We assessed manifestations associated with a rare 3' untranslated region mutation (UTR) of GJB1 in a large family with X-linked Charcot-Marie-Tooth disease (CMTX).Methods: Clinical, electrophysiological, and molecular genetic analyses were performed on an 8-generation family with CMTX.Results: There were 22 affected males and 19 symptomatic females, including an 83-year-old woman followed for 40 years. Electrophysiological studies showed a primarily axonal neuropathy. The c.*15C>T mutation in the GJB1 3' UTR was identified in 4 branches of the family with a log of odds (LOD) of 4.91. This created a BstE II enzyme recognition site that enabled detection by restriction digestion.Discussion: The c.*15C>T mutation in the GJB1 3' UTR segregates with CMTX1 in 8 generations. Penetrance in males and females is essentially complete. A straightforward genetic method to detect this mutation is described. Muscle Nerve 57: 859-862, 2018. [ABSTRACT FROM AUTHOR]

The average daily gain (ADG) and body weight (BW) are very important traits for breeding programs and for the meat production industry, which have attracted many researchers to delineate the genetic architecture behind these traits. In the present study, single‐ and multi‐trait genome‐wide association studies (GWAS) were performed between imputed whole‐genome sequence data and the traits of the ADG and BW at different stages in a large‐scale White Duroc × Erhualian F2 population. A bioinformatics annotation analysis was used to assist in the identification of candidate genes that are associated with these traits. Five and seven genome‐wide significant quantitative trait loci (QTLs) were identified by single‐ and multi‐trait GWAS, respectively. Furthermore, more than 40 genome‐wide suggestive loci were detected. On the basis of the whole‐genome sequence association study and the bioinformatics analysis, NDUFAF6, TNS1 and HMGA1 stood out as the strongest candidate genes. The presented single‐ and multi‐trait GWAS analysis using imputed whole‐genome sequence data identified several novel QTLs for pig growth‐related traits. Integrating the GWAS with bioinformatics analysis can facilitate the more accurate identification of candidate genes. Higher imputation accuracy, time‐saving algorithms, improved models and comprehensive databases will accelerate the identification of causal genes or mutations, which will contribute to genomic selection and pig breeding in the future. [ABSTRACT FROM AUTHOR]

Objectives: Determine ancillary test utilization for the workup of isolated eosinophilia in otherwise morphologically unremarkable bone marrow (BM).Methods: We evaluated BM ancillary testing performed in cases with isolated eosinophilia and otherwise morphologically unremarkable BM. Cases with abnormal morphology (eg, dysplasia, basophilia) and/or findings suggestive of a disorder (eg, unexplained thromboses, lymphoma) are specifically excluded.Results: A total of 132 cases met inclusion criteria. Ten cases had an ancillary testing abnormality that warranted a more specific hematologic diagnosis: four cases of lymphocytic variant of hypereosinophilic syndrome, three cases of myeloid neoplasm with PDGFRA rearrangement, and one case each of myeloid neoplasm with PDGFRB rearrangement, chronic eosinophilic leukemia, and morphologically occult systemic mastocytosis. No cases revealed a cryptic PDGFRB or BCR/ABL1 rearrangement or JAK2 V617F mutation.Conclusions: Findings from our institutional experience support initial testing in isolated eosinophilia with otherwise unremarkable BM to include PDGFRA rearrangement, tryptase/CD25 immunohistochemistry, cytogenetics, and T-cell flow cytometry/receptor gene rearrangement. This approach achieves diagnostic quality and test utilization efficiency in our clinical practice. [ABSTRACT FROM AUTHOR]

The article discusses research which examined the adult and pediatric bone marrow failure syndrome database at the Mayo Clinic from 1990-2016 for patients with inherited bone marrow failure syndrome (IBMFS). Topics covered include the analysis of the electronic medical record for germline disorders, the demographic characteristics, clinical correlates, details on myeloid clonal evolution and outcomes, and outcomes of allogeneic stem cell transplantation.

The article presents a case study of a 29-year-old female with chronic thrombocytopenia. Topics discussed include flow cytometry and platelet transmission electron microscopy (PTEM) performed using clinically validated laboratory tests, germline heterozygous RUNX1 mutations causing autosomal dominant, and the clinical phenotype of patients with germline RUNX1 mutations found to be heterogeneous.

Combined alpha-delta platelet storage pool deficiency is characterized by the absence or reduction in the number of both alpha granules and dense bodies. This disorder can have variable severity as well as a variable inheritance pattern. We describe two patients from unrelated families with combined alpha-delta storage pool deficiency due to mutations in GFI1B , a zinc finger protein known to act as a transcriptional repressor of various genes. We demonstrate that this disease is associated with either a heterozygous mutation (de novo or familial) abrogating the binding of the zinc fingers with the promoter of its target genes, or by hypomorphic biallelic mutations in GFI1B leading to autosomal recessive inheritance. [ABSTRACT FROM AUTHOR]

The clinical and laboratory characteristics of patients with non-syndromic, autosomal dominant thrombocytopenia secondary to germ lineANKRD26mutations appear to be heterogeneous. Except for a targeted molecular genotyping approach, there is no distinct clinical or laboratory phenotype that has been specifically associated with this particular gene mutation. Such heterogeneity could be due to variations in mutation and genetic background in different families. To understand the phenotypic heterogeneity, we thoroughly studied one affected family using the International Society for Thrombosis and Haemostasis bleeding assessment tool and both clinically validated standard and esoteric platelet testing (electron microscopy (EM) and flow cytometry). We found that decreased platelet aggregation with arachidonic acid and epinephrine agonists was common in affected family members. EM studies demonstrated persistent borderline low mean dense granules per platelet, decreased alpha granules and an increased canalicular network pattern in all affected members. Since these characteristics are subtle or non-pathognomonic, molecular testing forANKRD26mutation remains the most reliable test to render a diagnosis and should be considered when evaluating a patient or family with congenital thrombocytopenia, particularly if there is a history of myeloid neoplasms. [ABSTRACT FROM PUBLISHER]

Objectives Mutations in MT-TS1 have been found to be associated with nonsyndromic sensorineural hearing loss (SNHL). PCDH15 codes for protocadherin-15, a member of the cadherin superfamily of calcium-dependent cell-cell adhesion molecules. In this study, we analyzed the correlation of both MT-TS1 and PCDH15 mutations in a Chinese Han family segregating maternally inherited nonsyndromic SNHL. Methods We ascertained a Chinese Han family segregating maternally inherited nonsyndromic sensorineural hearing loss. Eight of 10 maternal members in this family exhibited late-onset, progressive hearing impairment. Mutation screening of 79 known deafness genes was performed for the proband by targeted next-generation sequencing. Results A total of 651 variants were detected in this individual. Among them, a homoplasmic 7511T>C variant in MT-TS1 , the mitochondrial tRNA Ser(UCN) gene, and a heterozygous p.Asp1010Gly variant in PCDH15 were more likely to be pathogenic. Consistent with the matrilineal inheritance with reduced penetrance, the 7511T>C variant in MT-TS1 was found in all 10 maternal members and an additional heterozygous p.Asp1010Gly variant in PCDH15 cosegregated with the hearing loss in this family. Conclusion Our results suggested that the PCDH15 p.Asp1010Gly variant probably modified the phenotypic expression of the 7511T>C mutation in MT-TS1 . [ABSTRACT FROM AUTHOR]

Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A/B protein as a novel regulator for pre-mRNA 3′-end processing in Arabidopsis. Genetic analysis reveals that HLP1 suppresses Flowering Locus C (FLC), a key repressor of flowering in Arabidopsis. Genome-wide mapping of HLP1-RNA interactions indicates that HLP1 binds preferentially to A-rich and U-rich elements around cleavage and polyadenylation sites, implicating its role in 3′-end formation. We show HLP1 is significantly enriched at transcripts involved in RNA metabolism and flowering. Comprehensive profiling of the poly(A) site usage reveals that HLP1 mutations cause thousands of poly(A) site shifts. A distal-to-proximal poly(A) site shift in the flowering regulator FCA, a direct target of HLP1, leads to upregulation of FLC and delayed flowering. Our results elucidate that HLP1 is a novel factor involved in 3′-end processing and controls reproductive timing via targeting APA. [ABSTRACT FROM AUTHOR]

Background: BRAF mutations have been well described in non-small cell lung cancer (NSCLC) for several years, but the clinical features of patients harboring BRAF mutations are still not well described. We performed a meta-analysis to identify common clinical features in NSCLC patients carrying BRAF mutations. Methods: We identified clinical studies that examined the association between BRAF mutations and features of NSCLC within PubMed, Embase and ISI Science Citation Index database up to October 2013. The effect size of clinical features was estimated by odds ratios (ORs) with 95% confidence interval (CI) for each study, using a fixed-effects or random-effects model. Results: Ten studies with a total of 5599 NSCLC patients were included. There was a 3% (170/5599) BRAF mutation rate. BRAF mutations in NSCLC were significantly associated with adenocarcinomas (ADCs) (compared with non-ADCs, OR = 4.96, 95%CI = 2.29–10.75). There were no significant differences in gender, smoking and stage in patients with and without BRAF mutations. The BRAFV600E mutation was more frequent in women than non-BRAFV600E mutations (OR = 0.27, 95%CI = 0.12–0.59), and was closely related to never smokers (OR = 0.14, 95%CI = 0.05–0.42). Conclusions: These findings have important implications for the prediction of the NSCLC sub-types more accurately combined with other genetic changes. [ABSTRACT FROM AUTHOR]

The response to epidermal growth factor receptor (EGFR)-targeted therapy in metastatic colorectal cancer (mCRC) is variable because of intra-tumor heterogeneity at the genetic level, and consequently, it is important to develop sensitive and selective assays to predict patient responses to therapy. Low-abundance BRAF V600E mutations are associated with poor response to treatment with EGFR inhibitors. We developed a method for the detection of BRAF V600E mutations in mCRC using real-time wild-type blocking PCR (WTB-PCR), in which a chimera composed of locked nucleic acids and DNA is incorporated to amplify the mutant allele at high efficiency while simultaneously inhibiting the amplification of wild-type alleles. Mixing experiments showed that this method is exquisitely sensitive, with detection of the mutated allele at a mutant/wild-type ratio of 1:10,000. To demonstrate the applicability of this approach for mCRC patients, we assessed the V600E mutations in 50 clinical cases of mCRC by real-time WTB-PCR. The percentage of patients with V600E mutation as determined by WTB-PCR (16 %, 8/50) was higher than by traditional PCR (10 %, 5/50), suggesting an increased sensitivity for WTB-PCR. By calculating the Δ C for real-time traditional PCR, which amplifies all BRAF alleles, versus WTB-PCR, which selectively amplifies mutant BRAF, we demonstrated that among the V600E-positive mCRC patient samples, the percentage of BRAF DNA with the V600E mutation ranged from 0.05 to 52.32 %. In conclusion, WTB-PCR provides a rapid, simple, and low-cost method to detect trace amounts of mutated BRAF V600E gene. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer (CRC) is a heterogeneous disease with multiple underlying causative genetic mutations. The B-type Raf proto-oncogene (BRAF) plays an important role in the mitogen-activated protein kinase (MAPK) signaling cascade during CRC. The presence of BRAFV600E mutation can determine the response of a tumor to chemotherapy. However, the association between the BRAFV600E mutation and the clinicopathological features of CRC remains controversial. We performed a systematic review and meta-analysis to estimate the effect of BRAFV600E mutation on the clinicopathological characteristics of CRC. Methods: We identified studies that examined the effect of BRAFV600E mutation on CRC within the PubMed, ISI Science Citation Index, and Embase databases. The effect of BRAFV600E on outcome parameters was estimated by odds ratios (ORs) with 95% confidence intervals (CIs) for each study using a fixed effects or random effects model. Results: 25 studies with a total of 11,955 CRC patients met inclusion criteria. The rate of BRAFV600 was 10.8% (1288/11955). The BRAFV600E mutation in CRC was associated with advanced TNM stage, poor differentiation, mucinous histology, microsatellite instability (MSI), CpG island methylator phenotype (CIMP). This mutation was also associated with female gender, older age, proximal colon, and mutL homolog 1 (MLH1) methylation. Conclusions: This meta-analysis demonstrated that BRAFV600E mutation was significantly correlated with adverse pathological features of CRC and distinct clinical characteristics. These data suggest that BRAFV600E mutation could be used to supplement standard clinical and pathological staging for the better management of individual CRC patients, and could be considered as a poor prognostic marker for CRC. [ABSTRACT FROM AUTHOR]

Abstract: Objectives: To characterize the clinical features of a Chinese DFNA9 family associated with a novel COCH mutation and to confirm the proposed genotype–phenotype correlation of COCH. Methods: Mutation screening of 79 deafness genes was performed in the proband by targeted next-generation sequencing. Co-segregation of the disease phenotype and the detected variants was confirmed in all family members by PCR amplification and Sanger sequencing. The progression of hearing impairment in affected family members was followed and the concomitant vestibular dysfunction was verified by the caloric vestibulo-ocular reflex test. Results: A novel COCH mutation p.G87V was identified in the family segregating with late-onset, progressive sensorineural hearing impairment and consistent vestibular dysfunction. Conclusion: The p.G87V mutation leads to a very similar phenotype as a previously reported p.G87W mutation of COCH. Our study suggested that the G87 residue is critical for function of COCH and further confirms a previously proposed genotype–phenotype correlation for DFNA9. [Copyright &y& Elsevier]

Background: Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary renal disorder. In most cases, ADPKD similarly affects bilateral kidneys. Case presentation: Among the 605 ADPKD patients that were followed up by our center, we identified two male patients with unilateral ADPKD. The cases were remarkable because the patients also had ectopia and multicystic dysplasia in the contralateral kidney, which are generally sporadic disease conditions. Both patients tested positive for polycystic kidney disease 1 mutation, but negative for hepatocyte nuclear factor 1 beta mutation. Moreover, the deterioration of their kidney function seemed to be quicker than their age- and sex-matched controls and siblings. Both patients had started a long-term hemodialysis in their 40s. Conclusion: Anatomical and genetic abnormality in patients with ADPKD may be more frequent and complex than previously believed. The compensatory capacity in patients with ADPKD is fragile, and missing one kidney could accelerate the deterioration of renal function. [ABSTRACT FROM AUTHOR]

Tooth agenesis is one of the most common developmental disorders in humans. Previous studies have attributed non-syndromic tooth agenesis to mutations in several genes, including MSX1, PAX9, EDA, and AXIN2. In this study, we investigated a Chinese family with tooth agenesis combined with cleft lip. Genomic DNA was isolated from blood samples of all available family members. Candidate genes MSX1 and PAX9 were amplified by the PCR and directly sequenced. A novel heterozygous mutation at c.C565T, exon 2 of MSX1, was identified in affected members. To analyze the effect of the nonsense mutation on MSX1 expression, vectors containing wild-type and mutated MSX1 were constructed and transfected into COS7 cell lines. Real-time PCR showed that the mRNA expression of the mutated MSX1 was dramatically reduced compared with that of the wild-type MSX1. Our findings suggest that the nonsense mutation in MSX 1 might have resulted in rapid degradation of the mutated transcript and caused the phenotype of tooth agenesis with cleft lip in the Chinese family. [ABSTRACT FROM AUTHOR]

Abstract: An X-linked myopathy was recently associated with mutations in the four-and-a-half-LIM domains 1 (FHL1) gene. We identified a family with late onset, slowly progressive weakness of scapuloperoneal muscles in three brothers and their mother. A novel missense mutation in the LIM2 domain of FHL1 (W122C) co-segregated with disease in the family. The phenotype was less severe than that in other reported families. Muscle biopsy revealed myopathic changes with FHL1 inclusions that were ubiquitin- and desmin-positive. This mutation provides additional evidence for X-linked myopathy caused by a narrow spectrum of mutations in FHL1, mostly in the LIM2 domain. Molecular dynamics (MD) simulations of the newly identified mutation and five previously published missense mutations in the LIM2 domain revealed no major distortions of the protein structure or disruption of zinc binding. There were, however, increases in the nonpolar, solvent-accessible surface area in one or both of two clusters of residues, suggesting that the mutant proteins have a variably increased propensity to aggregate. Review of the literature shows a wide range of phenotypes associated with mutations in FHL1. However, recognizing the typical scapuloperoneal phenotype and X-linked inheritance pattern will help clinicians arrive at the correct diagnosis. [ABSTRACT FROM AUTHOR]

GIF, a member of the metallothionein (MT) family (assigned as MT3), is a neuron growth inhibitory factor that inhibits neuron outgrowth in Alzheimer’s disease. The conserved Thr5 is one of the main differences between GIF and other members in the MT family. However, natural sheep GIF has an unusual Ala5, casting doubt on the role of common Thr5. We constructed a series of human GIF mutants at site 5, and characterized their biochemical properties by UV spectroscopy, circular dichroism spectroscopy, EDTA reaction, 5,5′-dithiobis(2-nitrobenzoic acid) (DTNB) reaction, and pH titration. Their inhibitory activity toward neuron survival and neurite extension was also examined. Interestingly, the T5A mutant exhibited distinct metal thiolate activity in the EDTA and DTNB reactions, and also lost its bioactivity. Meanwhile, the T5S mutant had similar biochemical properties and biological activity as wild-type human GIF, indicating the hydroxyl group on the Thr5 was critical to the bioactivity of human GIF. We suggest the hydroxyl group in human GIF may help stabilize the biologically active conformation. On the other hand, lack of the hydroxyl group in sheep GIF may be partially compensated by its abnormal structure. [ABSTRACT FROM AUTHOR]

Background: Vacuolar protein sorting-associated protein 4B (VPS4B) is a member of the ATP enzyme AAA protein family, and is mainly involved in protein degradation and cell membrane fusion. Recently, a dominant mutation in this gene was identified in human dentin dysplasia type I (DD-I). Herein, we report the generation of Vps4b knockout (Vps4b KO) mice; however, the homozygous Vps4b KO mutation was embryonic lethal at the early stages of embryo development, and we therefore report the results of heterozygous mutant mice. Results: Mice heterozygous for Vps4b did not develop tooth defects replicating human DD-I. Immunohistochemistry showed that gene KO was successful, as there was decreased expression of Vps4b in heterozygous mice; hematoxylin and eosin (H&E) staining also showed that the width of the pre-dentin zone was increased in heterozygous mice, although the arrangement of the odontoblasts was not significantly different from wild-type (WT) mice. However, H&E staining showed no obvious abnormalities in the bones of heterozygous mice. Moreover, stereomicroscopic and X-ray radiography results indicated no abnormal manifestations in teeth or bones. Furthermore, statistical analysis of the volume and density of dentin and enamel, as well as skeletal analysis, including the volume and separation of trabecular bone analyzed by micro-CT, all showed no differences between Vps4b heterozygotes and WT mice. In addition, there also were no significant differences in bone or cartilage mineralization as evaluated by Alcian blue–Alizarin red staining. Conclusions: The heterozygous Vps4b KO mice do not develop tooth defects that replicate human DD-I and this is likely to be due to differences in tooth development between the two species. Consequently, further studies are needed to determine whether mice are an appropriate animal model for human tooth diseases. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the article "Co-existence of JAK2 V617F and CALR mutations in primary myelofibrosis" by L. Zamora and colleagues in the 2015 issue.

Aims The purpose of this study was to identify the genetic causes of a family presenting with multiple symptoms overlapping Usher syndrome type II (USH2) and Waardenburg syndrome type IV (WS4). Methods Targeted next-generation sequencing including the exon and flanking intron sequences of 79 deafness genes was performed on the proband. Co-segregation of the disease phenotype and the detected variants were confirmed in all family members by PCR amplification and Sanger sequencing. Results The affected members of this family had two different recessive disorders, USH2 and WS4. By targeted next-generation sequencing, we identified that USH2 was caused by a novel missense mutation, p.V4907D in GPR98 ; whereas WS4 due to p.V185M in EDNRB . This is the first report of homozygous p.V185M mutation in EDNRB in patient with WS4. Conclusion This study reported a Chinese family with multiple independent and overlapping phenotypes. In condition, molecular level analysis was efficient to identify the causative variant p.V4907D in GPR98 and p.V185M in EDNRB , also was helpful to confirm the clinical diagnosis of USH2 and WS4. [ABSTRACT FROM AUTHOR]

Introduction: Vitamin D is significantly associated with virus replication in chronic hepatitis B virus (HBV) infection. However, the relationship between low serum vitamin D levels and HBV "a" determinant mutations remains unknown. Methodology: A total of 133 chronically HBV-infected, treatment-naive patients were randomly selected in the present study. Serum vitamin D levels were measured by using liquid chromatography-mass spectrometry. The HBV "a" determinant was amplified, sequenced, and analyzed by nested polymerase chain reaction (PCR). Results: Among 133 patients, 36, 88, and 9 patients had vitamin D deficiency (25(OH)D < 14 ng/mL), vitamin D insufficiency (25(OH)D ≥14 and < 30 ng/mL), and normal vitamin D serum levels ((25(OH)D = 30 ng/mL), respectively. As results showed, 36 [11 genotype B HBVs (HBV/B) and 25 genotype C HBVs (HBV/C)] were isolated from the vitamin D-deficient group, 88 (48 HBV/B and 40 HBV/C) from the vitamin D-insufficient group, and 4 HBV/C strains from the normal serum-vitamin D group. Compared to the HBV/B infected patients with vitamin D insufficiency, higher rates of amino acid mutation within "a" determinant were detected in HBV/B-infected, vitamin D-deficient patients. Moreover, the change frequency of M133 was 27.27% in HBV/B infected patients with vitamin D deficiency, which was significantly higher than those in the vitamin D-insufficient group (p = 0.040). Conclusions: Vitamin D deficiency is significantly associated with genotype B HBV "a" determinant mutations. [ABSTRACT FROM AUTHOR]

Highlights: [•] BAG2 colocalizes with PINK1 and R492X PINK1 mutation in vivo. [•] BAG2 binds with PINK1 directly and stabilizes PINK1 by decreasing its ubiquitination. [•] BAG2 also binds with R492X PINK1 mutation, directly and more tightly. [•] BAG2 stabilizes R492X PINK1 mutation by decreasing its ubiquitination more obviously. [Copyright &y& Elsevier]

Aim: Genomic alterations and somatic mutations have been widely identified in hematologic malignancies. Recent studies have described mutations in different HLA genes of these patients. These mutations are identified when high resolution typing is needed for patients and potential donors. An African American patient treated for myeloma, received an autologous stem cell transplant in 2010. During 2011 he was diagnosed with a secondary plasma cell leukemia, becoming a candidate for an allogeneic stem cell transplant. Methods: HR HLA typing was performed by Sequence Based Typing (SBT) methodology and a single base mismatch on one of his HLA-DQB1 allele was identified in exon 2, codon 13, leading to an amino acid substitution (Glycine to Valine). Three siblings, considered potential donors, had HLA typing performed and the same HLA-DQB1∗06:XX was identified in two of them. To investigate the HLA-DQB1 novel allele segregation and its origin within the family, their mother was typed. Results: One of the HLA-DQB1 alleles identified did not match with DQB1 alleles from HLA database 3.6.0, used for the SBT data analysis. Their mother HLA typing identified HLA-DQB1∗06:02:01 and DQB1∗06:XX. The alleles DQB1∗06:XX and DQB1∗06:02:01 differ by 1 nucleotide mismatch in exon 2, which caused us to question what genetic alterations that may have occurred in her DQB1 genes. Conclusions: Our findings demonstrate that the hematological malignancy is not always the cause for HLA genes alterations, which reinforces the value of family studies to explain gene segregation. Beyond the implications of obtaining an accurate HLA typing and donor selection, these genetic alterations on HLA genes may allow some mechanisms of immune surveillance to fail when associated with other complications caused by hematological malignancies affecting bone marrow transplant candidates. The allele in question was also identified by another HLA laboratory, and is included in the most recent IMGT HLA alleles update, it was named HLA-DQB1∗06:49. [Copyright &y& Elsevier]