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The identification of oncogenic gene fusions in diffuse gliomas may serve as potential therapeutic targets and prognostic indicators, representing a novel strategy for treating gliomas consistent with the principles of personalized medicine. This study identified detectable oncogene fusions in glioma patients through an integrated analysis of genomic and transcriptomic data, which encompassed whole exon sequencing and next-generation RNA sequencing. In addition, this study also conducted a comparison of the genetic characteristics, tumor microenvironment, mutation burden and survival between glioma patients with or without gene fusions. A total of 68 glioma patients were enrolled in this study, including glioblastoma (GBM), low grade glioma (LGG) and diffuse midline glioma (DMG). 14 cases of GBM patients (51.9%, 14/27) were found to harbor the following 70 oncogenic gene fusions: ROS1 (n = 8), NTRK (n = 5), KIF5 (n = 5), RET (n = 3) and other infrequent gene fusions (n = 49). A total of 11 gene fusions were identified in 8 LGG patients (32.0%, 8/25) and seven gene fusions were identified in one DMG patient (16.7%, 1/6). In GBM patient group, five genes including HOXA3, ACTB, CDK5, GNA12 and CARD11 exhibited a statistically significant higher copy number amplification frequency in the GBM group without gene fusions compared to that in the GBM group with gene fusions. In LGG patient group, CDK5 gene was also found to exhibit a statistically significant higher amplification frequency in the LGG group without gene fusions. In addition, KMT2D exhibited a statistically significant higher mutation frequency in the LGG group with gene fusions compared to that in the LGG group without gene fusions. Comparison of the other genetic characteristics including immune cell infiltration score, tumor mutation burden (TMB), and microsatellite instability (MSI). The results showed no statistically significant differences were observed between fusion and non-fusion group of GBM and LGG. The survival analysis revealed that GBM patients without gene fusions exhibited a longer median survival (737 days) compared to GBM patients with gene fusions (642 days), but without a statistical significancy. Our study has identified a set of gene fusions present in gliomas, including a number of novel gene fusions that have not been previously reported. We have also elucidated the underlying genetic characteristics of glioma with gene fusions. Collectively, our findings have the potential to inform future clinical treatment strategies for patients with glioma. [ABSTRACT FROM AUTHOR]

Abstract The identification of oncogenic gene fusions in diffuse gliomas may serve as potential therapeutic targets and prognostic indicators, representing a novel strategy for treating gliomas consistent with the principles of personalized medicine. This study identified detectable oncogene fusions in glioma patients through an integrated analysis of genomic and transcriptomic data, which encompassed whole exon sequencing and next-generation RNA sequencing. In addition, this study also conducted a comparison of the genetic characteristics, tumor microenvironment, mutation burden and survival between glioma patients with or without gene fusions. A total of 68 glioma patients were enrolled in this study, including glioblastoma (GBM), low grade glioma (LGG) and diffuse midline glioma (DMG). 14 cases of GBM patients (51.9%, 14/27) were found to harbor the following 70 oncogenic gene fusions: ROS1 (n = 8), NTRK (n = 5), KIF5 (n = 5), RET (n = 3) and other infrequent gene fusions (n = 49). A total of 11 gene fusions were identified in 8 LGG patients (32.0%, 8/25) and seven gene fusions were identified in one DMG patient (16.7%, 1/6). In GBM patient group, five genes including HOXA3, ACTB, CDK5, GNA12 and CARD11 exhibited a statistically significant higher copy number amplification frequency in the GBM group without gene fusions compared to that in the GBM group with gene fusions. In LGG patient group, CDK5 gene was also found to exhibit a statistically significant higher amplification frequency in the LGG group without gene fusions. In addition, KMT2D exhibited a statistically significant higher mutation frequency in the LGG group with gene fusions compared to that in the LGG group without gene fusions. Comparison of the other genetic characteristics including immune cell infiltration score, tumor mutation burden (TMB), and microsatellite instability (MSI). The results showed no statistically significant differences were observed between fusion and non-fusion group of GBM and LGG. The survival analysis revealed that GBM patients without gene fusions exhibited a longer median survival (737 days) compared to GBM patients with gene fusions (642 days), but without a statistical significancy. Our study has identified a set of gene fusions present in gliomas, including a number of novel gene fusions that have not been previously reported. We have also elucidated the underlying genetic characteristics of glioma with gene fusions. Collectively, our findings have the potential to inform future clinical treatment strategies for patients with glioma.

Shuqi Huang,* Moath abbas abdalla alhadidi,* Nanfei Feng, Chuan Wan Department of Dermatology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, People’s Republic of China*These authors contributed equally to this workCorrespondence: Chuan Wan, Department of Dermatology, The First Affiliated Hospital of Nanchang University, Yong Wai Zheng Street 17#, Nanchang, 330006, People’s Republic of China, Tel +86-18070052970, Email chuanwan@ncu.edu.cnAbstract: Papular acantholytic dyskeratosis (PAD), often found to occur in the vulvar or anogenital area, is an exceedingly rare skin condition that usually presents in adulthood and features multiple smooth skin-colored or grayish-white papules with or without pruritus. Although the pathogenesis of PAD is unknown, PAD may be associated with mutations in ATP2C1 and ATP2A2 genes. Here, we report on an 18-year-old female patient with multiple gray-white flat papules in the anogenital area. Skin biopsy revealed hyperkeratosis of the epidermis, acantholysis, formation of fissures or lacunae, and disappearance of desmosomes. Whole exon sequencing (WES) of the patient indicated mutations in the ATP2C1 gene.Keywords: Papular acantholytic dyskeratosis, Whole exon sequencing, ATP2C1

ObjectiveTo describe the clinical presentation and novel mutation in the ganglioside-beta-galactosidase gene (GLB1) gene in a Chinese family with GM1 gangliosidosis.MethodsWe collected clinical data from a Chinese family with GM1 gangliosidosis, and performed whole exon sequencing (WES) of the proband and his parents. The pathogenic sites of candidate genes were targeted, and the detected exon mutations were verified by Sanger sequencing. Enzyme activity of β-galactosidase was detected in 293T cells transiently transfected with plasmids encoding the detected mutations.ResultsTwo siblings in this family presented with neurological degeneration, and were classified as the late-infantile type. Two siblings and their parents underwent WES of the peripheral blood. A reported missense mutation c.446C>T and a novel mutation c.1058_1059delinsAA in GLB1 gene inherited from the mother and father respectively were identified. The mutant c.1058_1059delinsAA retained β-galactosidase activity at 0% of wild-type GLB1.ConclusionThis study identified a novel mutation of the GLB1 gene in a Chinese family with GM1 gangliosidosis and provided new insights into the molecular characteristics and genetic counseling of GM1 gangliosidosis.

Objective: To present the ultrasound imaging and genetic diagnosis of a fetus with prenatal lethal form of Gaucher disease. Case report: A 37-year-old primiparous woman was pregnant at her 23 weeks of gestation and the prenatal fetal ultrasound revealed hydrops fetalis, cerebellum hypoplasia, and fetal immobility. The pregnancy was terminated due to major fetal anomaly, and whole exome sequencing (WES) analysis of fetal tissue and parental blood unveiled a pathogenic variant in exon 10 of the GBA gene (NM_001005741.3: c.1265T > G: p.L422R) originating from the mother. Additionally, a novel CNV (chr1: 155204785–155205635 deletion, 0.85 kb) spanning exon 10–12 in the GBA gene was identified from the father. This compound heterozygosity confirmed the diagnosis of prenatal lethal form of Gaucher disease and was informative for genetic counseling. Conclusion: WES is a powerful tool to detect pathogenic variants among fetuses with nonimmune hydrops fetalis and complex abnormality from prenatal ultrasound. Compound heterozygosity consisted of single nucleotide variants (SNV) and copy number variations (CNVs) may lead rare inherited metabolic disorders including prenatal lethal form of Gaucher disease.

Objective : To explore disease-related mutations and its effect on disease in the population through high-throughput gene screening of the members of an early-onset Parkinson's disease (EOPD) genetic family. Methods : SNP microarray and whole exon sequencing (WES) were performed in 19 members of early-onset PD genetic families. Moreover, the sequencing of 58 sporadic patients was verified to screen out mutation genes with high risk. Results : Linkage analysis found 3 chromosome regions, and WES and coexpression analysis screened out 24 genes that may be associated with PD. The Spearman correlation coefficient R>0.6 and P<0.05 between five loci genotype and disease outcome indicated that there was a correlation. Conclusion : Through multilevel mutation .site .screening analysis in clinical patients, we find that five mutant genes Pdxdcl, Ddx56, Aspn, Rbm28 and Shisa9 in exon region may be closely associated with PD. More functional research will be conducted in the future. [ABSTRACT FROM AUTHOR]

The case report by Mabry et al. (1970) of a family with four children with elevated tissue non-specific alkaline phosphatase, seizures and profound developmental disability, became the basis for phenotyping children with the features that became known as Mabry syndrome. Aside from improvements in the services available to patients and families, however, the diagnosis and treatment of this, and many other developmental disabilities, did not change significantly until the advent of massively parallel sequencing. As more patients with features of the Mabry syndrome were identified, exome and genome sequencing were used to identify the glycophosphatidylinositol (GPI) biosynthesis disorders (GPIBDs) as a group of congenital disorders of glycosylation (CDG). Biallelic variants of the phosphatidylinositol glycan (PIG) biosynthesis, type V (PIGV) gene identified in Mabry syndrome became evidence of the first in a phenotypic series that is numbered HPMRS1-6 in the order of discovery. HPMRS1 [MIM: 239300] is the phenotype resulting from inheritance of biallelic PIGV variants. Similarly, HPMRS2 (MIM 614749), HPMRS5 (MIM 616025) and HPMRS6 (MIM 616809) result from disruption of the PIGO, PIGW and PIGY genes expressed in the endoplasmic reticulum. By contrast, HPMRS3 (MIM 614207) and HPMRS4 (MIM 615716) result from disruption of post attachment to proteins PGAP2 (HPMRS3) and PGAP3 (HPMRS4). The GPI biosynthesis disorders (GPIBDs) are currently numbered GPIBD1-21. Working with Dr. Mabry, in 2020, we were able to use improved laboratory diagnostics to complete the molecular diagnosis of patients he had originally described in 1970. We identified biallelic variants of the PGAP2 gene in the first reported HPMRS patients. We discuss the longevity of the Mabry syndrome index patients in the context of the utility of pyridoxine treatment of seizures and evidence for putative glycolipid storage in patients with HPMRS3. From the perspective of the laboratory innovations made that enabled the identification of the HPMRS phenotype in Dr. Mabry's patients, the need for treatment innovations that will benefit patients and families affected by developmental disabilities is clear. [ABSTRACT FROM AUTHOR]

Objective To analyze the clinical characteristics and genotype of a patient with congenital systemic lipodystrophy (CGL) type 1 associated with exudative xanthoma caused by AGPAT2 gene mutation, and to provide evidence for clinical and genetic diagnosis of the disease.Methods Clinical data of the patient such as medical history, physical examination and laboratory examination were collected. Peripheral venous blood was collected for whole exome sequencing analysis and Sanger sequencing verification, and treatment was provided to patients according to the changes of condition. Results The clinical manifestations of the patient were subcutaneous fat reduction, fatty liver, spleen enlargement, kidney enlargement, high blood sugar and lipids, severe insulin resistance, scattered yellow rash on limbs, which was confirmed as xanthoma. The results of whole exon sequencing showed that the AGPAT2 gene of the patient had a heterozygous nonsense mutation of c.202C＞T:p.R68* and c.646A＞T:p.K216*, and the former was the pathogenic mutation site. Follow-up therapy covers improvement of lifestyle, low-fat diet and regular exercise. The rashes subsided after active lipid-lowering therapy. Conclusions Apart from typical lipody-strophy, the patient was accompanied by exanthemous xanthoma. No CGL1 patient with exanthemous xanthoma has been reported in the domestic literature database up to now, and the genetic test results showed that there was a c.202C＞T heterozygous mutation of AGPAT2 gene. This gene site has not been reported in the literature, and its functional verification needs to be further studied.

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Abstract Introduction The number of patients with synchronous multiple primary lung cancer (sMPLC) has increased recently. However, diagnosing and selecting the appropriate therapeutic strategy for this type of disease is not simple. Case presentation This report presented a case of sMPLC with lymph node metastasis. With no smoking and cancer history, this patient had seven nodules in the right lung and underwent single-portal video-assisted thoracoscopic surgery (VATS). In addition, she received four cycles of chemotherapy after the operation. Whole exon sequencing (WES) was performed in five resected tissue samples (four tumors and one lymph node). We conducted genomic profiling and clone evolution analysis of the five samples. Gene detection helped to confirm that the metastasis lymph node was transferred from one nodule. There was apparent heterogeneity of gene mutations among the five samples of the patient, with only one shared “neurofilament heavy polypeptide” (NEFH) mutation. A dominant substitution of C > T/G > A was found in all the samples. Pyclone model was used to calculate all tissues' cellular prevalence (CP) values, and NEFH mutations were thought to be the ancestral clones. During the follow-up period, residual lesions showed no apparent changes and limited response to chemotherapy. Conclusions This report showed an essential role in genomic detection and selecting the appropriate treatment of sMPLC. Surgery remains the primary treatment strategy for this type of disease, and the occurrence and development of sMPLC need more in-depth research.

AIM: To identify the pathogenic gene in a family with primary open angle glaucoma(POAG)from Nantong, Jiang Province, and to analyze its clinical phenotype and pathogenic mechanism.METHOD: A POAG pedigree was reviewed and recruited from January 2020 to December 2020, which spans 5 generations, with 33 people in total. A total of 13 family members were enrolled in our study, of whom 4 members were diagnosed with POAG, 1 with ocular hypertension(OHT), and the other 8 members were unaffected. Detailed medical history was collected and a comprehensive ophthalmic examination was performed. High throughput sequencing was used to screen for possible pathogenic gene, and Sanger sequencing was used to verify candidate pathogenic gene.RESULT: All patients in this family were found to have elevated intraocular pressure(IOP)and diagnosed with glaucoma at a young age, requiring surgical treatments to control the IOP. The highest IOP of proband was up to 55mmHg. A heterozygous mutation(c.1197C>A, p.Phe399Leu)of LTBP2 gene was found in the proband genome by whole exon sequencing(WES). Sanger sequencing verified that the mutation was not isolated from the family disease.CONCLUSION: LTBP2 (c.1197C>A)mutation was not the pathogenic gene of POAG in this family. However, the pathogenic potential of LTBP2 gene in POAG cases is worth studying.

A comprehensive survey was carried out to investigate the genetic etiology of short stature in children by whole exon sequencing of a core family cohort to find and study mutations in multiple genes to assess their potential correlations to low height in children. The study included 56 pediatric patients from the Department of Pediatrics at the Zhangzhou Affiliated Hospital of Fujian Medical University. The participants met strict inclusion criteria, including age, Han Chinese ethnicity, low height standard deviation score, and the absence of known causes for short stature. Core pedigrees were identified using exome sequencing. After sequencing, variations were categorized and interpreted according to a variety of factors, including inheritance, location, type, and disease-causing gene databases. Variants were verified by Sanger sequencing. Most of the 97 gene mutations were missense. ACAN, PHEX, and COL2A1 were the most common gene mutations. Copy number variations were identified, particularly associated with the PHEX gene. Protein functional studies revealed that the mutations had a considerable influence on disease-promoting damage. The chromosomal locations with the highest enrichment of these genes were chr12, chr5, and chr2. In conclusion, the study revealed numerous genetic changes that may substantially impact physiological processes and disease. These findings establish the basis for further investigations into their diagnostic and therapeutic capabilities.

Background and aimsJoubert syndrome (JBTS, OMIM # 213300) is a group of ciliopathies characterized by mid-hindbrain malformation, developmental delay, hypotonia, oculomotor apraxia, and breathing abnormalities. Molar tooth sign in brain imaging is the hallmark for diagnosing JBTS. It is a clinically and genetically heterogeneous disorder involving mutations in more than 40 ciliopathy-related genes. However, long-term follow-up data are scarce, and further research is needed to determine the abundant phenotypes and genetics of this disorder. The study aimed to summarize clinical manifestations, particular appearance on cranial imaging, genetic data, and prognostic features of patients with JBTS.MethodsA retrospective case review of 36 cases of JBTS from May 1986 to December 2021 was performed. Clinical data of JBTS patients with development retardation and molar tooth sign on cranial imaging as the main features were analyzed. Genetic testing was performed according to consent obtained from patients and their families. The Gesell Developmental Scale was used to evaluate the intelligence level before and after treatment. The children were divided into a purely neurological JBTS (pure JBTS) group and JBTS with multi-organ system involvement group and then followed up every 3–6 months.ResultsWe enrolled 18 males and 18 females. Thirty-four (94.44%) cases had developmental delay, one patient (2.78%) had strabismus, and one patient (2.78%) had intermittent dizziness. There was one case co-morbid with Lesch-Nyhan syndrome. Three-quarters of cases had one or more other organ or system involvement, with a greater predilection for vision and hearing impairment. JBTS could also involve the skin. Thirty-one cases (86.11%) showed a typical molar tooth sign, and five cases showed a bat wing sign on cranial imaging. Abnormal video electroencephalogram (VEEG) result was obtained in 7.69% of cases. We found six JBTS-related novel gene loci variants: CPLANE1: c.4189 + 1G > A, c.3101T > C(p.Ile1034Thr), c.3733T > C (p.Cys1245Arg), c.4080G > A(p.Lys1360=); RPGRIP1l: c.1351-11A > G; CEP120: c.214 C > T(p.Arg72Cys). The CHD7 gene may be potentially related to the occurrence of JBTS. Analysis showed that the prognosis of pure JBTS was better than that of JBTS with neurological and non-neurological involvement after the formal rehabilitation treatment (P

Background: Infertility is a common and rapidly growing health issue around the world. The genetic analysis based on the infertile population is crucial for intervention and treatment. Objective: To find candidate gene locus led to azoospermia in Chinese multi-ethnic groups and provide theoretical guidance for the diagnosis of genetic diseases to progressively aggravated infertility patients and sterile offspring with ART. Methods: The study based on whole-exome sequencing (WES) was presented for genetic characteristic analysis of multi-ethnics and identification of variants related to infertility in Xinjiang area of China. Results: The frequency of pathogenic variants showed significant ethnic differences among four main ethnics in Xinjiang. The population structure analysis confirmed that the Hui was close to the Han population, the Kazak was close to the Uygur population, and there are three ancestry components in the four ethnics. In addition, ten candidate variants potentially regulated azoospermia were detected, and KNTC1 (rs7968222: G > T) was chosen to validate the association. Through the analysis in the valid group, the frequency of rs7968222 (G > T) has a significant difference in the azoospermia population (11.76%, 8/68) and normospermia population (4.63%, 35/756) (P < 0.001). Interestingly, the proportion of people with abnormal follicle-stimulating hormone (FSH) level in the group carrying rs7968222 (G > T) was significantly higher than non-carriers (P < 0.05). Therefore, rs7968222 may regulate spermatogenesis through affecting hormone level. Conclusion: Our study establishes the genetics analysis of Northwest China and finds a candidate gene locus KNTC1 (rs7968222: G > T), which is one of the genetic susceptibility factors for male azoospermia. [ABSTRACT FROM AUTHOR]

Yuting Wang,1 SongNian Hu,2 XinYu Tan,2 Qingqing Sang,3 Peng Shi,3 Chun Wang,3 Daoqian Sang3 1Department of Neurology, The Third Affiliated Hospital of Anhui Medical University, Heifei, People’s Republic of China; 2State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China; 3Department of Neurology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of ChinaCorrespondence: Daoqian Sang, Department of Neurology, The First Affiliated Hospital of Bengbu Medical College, 287, Changhuai Road, Bengbu, 233004, People’s Republic of China, Email sangdaoqian@bbmc.edu.cnPurpose: The aim of this study was to screen the possible pathogenic genes of one family with tuberous sclerosis complexes (TSCs).Patients and Methods: All family members were examined through detailed clinical evaluations, auxiliary examinations and CT. Then, we selected five members from this TSC family as the test samples. They were analysed by a new exon group sequencing method. Single nucleotide polymorphisms (SNPs) were screened by using databases, such as dbSNP and HAPMAP, and then the candidate genes were selected. Genes were analysed, and finally, the most likely mutation sites were screened. The results were examined by Sanger sequencing.Results: In this TSC family, we identified c.913+2T>G, a splicing site mutation in the 9th intron region of TSC1. Family members without TSC did not have this mutation.Conclusion: The mutations in the intron regions cannot be ruled out as a pathogenic factor for TSC.Keywords: pathogenic genes, tuberous sclerosis complex, whole exon sequencing, intron mutation

Introduction: The number of patients with synchronous multiple primary lung cancer (sMPLC) has increased recently. However, diagnosing and selecting the appropriate therapeutic strategy for this type of disease is not simple. Case presentation: This report presented a case of sMPLC with lymph node metastasis. With no smoking and cancer history, this patient had seven nodules in the right lung and underwent single-portal video-assisted thoracoscopic surgery (VATS). In addition, she received four cycles of chemotherapy after the operation. Whole exon sequencing (WES) was performed in five resected tissue samples (four tumors and one lymph node). We conducted genomic profiling and clone evolution analysis of the five samples. Gene detection helped to confirm that the metastasis lymph node was transferred from one nodule. There was apparent heterogeneity of gene mutations among the five samples of the patient, with only one shared "neurofilament heavy polypeptide" (NEFH) mutation. A dominant substitution of C > T/G > A was found in all the samples. Pyclone model was used to calculate all tissues' cellular prevalence (CP) values, and NEFH mutations were thought to be the ancestral clones. During the follow-up period, residual lesions showed no apparent changes and limited response to chemotherapy. Conclusions: This report showed an essential role in genomic detection and selecting the appropriate treatment of sMPLC. Surgery remains the primary treatment strategy for this type of disease, and the occurrence and development of sMPLC need more in-depth research. [ABSTRACT FROM AUTHOR]

Multiple primary cancers (MPCs) refer to cancers that occur simultaneously or metachronously in the same individual. The incidence of MPC has increased recently, as the survival time of malignant tumor patients has been greatly prolonged. It is difficult to differentiate MPC from primary cancers (PCs) in the same anatomical region from the clinical manifestation alone. However, their biological behaviors appear to be distinct. In this study, we show that the prognosis of multiple primary oral cancers (MP-OCs) is worse than primary oral cancers (P-OCs). To better understand the molecular mechanisms of MP-OC, we used whole exome sequencing (WES) to analyze samples from 9 patients with MP-OC and 21 patients with P-OC. We found more somatic mutations in MP-OC than in P-OC. MP-OC had more complicated mutation signatures, which were associated with age-related and Apolipoprotein B mRNA Editing Catalytic Polypeptide-like (APOBEC) activity-related signatures. Tumor mutational burden (TMB) and mutant-allele tumor heterogeneity (MATH) of MP-OC trended higher compared to P-OC. KEGG and GO analysis showed the differential pathways of MP-OC versus P-OC. In addition, MP-OC took amplification, not loss, as the main pattern of copy number variation (CNV), while P-OC took both. Lastly, we did not find significantly different mutant germline genes, but MSH-6 mutation may be a potential MP-OC driver. In short, our preliminary results show that MP-OC and P-OC have different molecular characteristics. [ABSTRACT FROM AUTHOR]

Objective To investigate the mutations in the tissue DNA and plasma circulating tumor DNA (ctDNA) from patients with prostate cancer, and analyze their association with clinical characteristics and treatment. Methods Based on probe hybridization capture and Illumina high-throughput sequencing, a targeted second-generation sequencing was used to analyze the mutations in 31 tumor tissues and 32 peripheral blood specimens from 46 patients with pathologically diagnosed prostate cancer. The tumor tissues and peripheral blood specimens were sequenced in the whole exons area and part of the introns area of 1 021 genes for 4 types of mutations (point mutation, loss/insert of small fragments, copy number variation and currently known fusion genes). Results The most frequently mutated gene was TP53 (29.0%, 9/31), followed by CDK12 (22.6%, 7/31), FOXA1 (22.6%, 7/31) and JAK1 (16.1%, 5/31) in 31 tissue samples. The most common mutant genes in the 32 blood samples were AR (34.3%, 11/32), APC (25.0%, 8/32), CDK12 (18.8%, 6/32), DNMT3a (18.8%, 6/32) and TP53 (18.8%, 6/32). TMPRSS2-ERG fusion gene was detected in 13.0% (6/46) of the 46 patients. One patient had TMPRSS2-ERG, VEGFA-TMPRSS2, and ERG-VEGFA fusion mutations simultaneously. The somatic mutation of homologous recombination (HR) associated genes were found in 21.7% (10/46) of all the patients, and those with germline mutations in the HR gene accounted for 8.7% (4/46) of all the patients. Moreover, the patients with HR gene mutations (either germline or somatic), especially those with germline mutations, had younger onset-age, higher Gleason score, and more metastases. Conclusion Gene mutation can be detected from both blood ctDNA and traditional tissue DNA. Dynamic blood ctDNA testing can monitor the changes in gene spectrum of prostate cancer, and is helpful to adjust treatment scheme in time.

Whole exon sequencing is a genomic analysis method that uses sequence capture technology to capture and enrich the whole genome exon region DNA for high-throughput sequencing. This technology has been applied to gene diagnosis and treatment of various complex diseases. At present, the pathogenesis of breast cancer has not been clearly elucidated, and the activation of oncogenes and the inactivation of tumor suppressor genes caused by gene mutation of somatic cells play a crucial role in the development of breast cancer. In recent years, numerous research groups have carried out a large number of whole exon sequencing researches, found and identified many genetic mutations associated with complex diseases/traits, which provide important clues for the study of the pathogenesis of complex diseases. This paper reviews the pathogenesis and diagnosis and treatment of breast cancer by whole exon sequencing.

Abstract Neoadjuvant chemotherapy (NACT) remains an attractive alternative for controlling locally advanced cervical cancer. However, approximately 15–34% of women do not respond to induction therapy. To develop a risk stratification tool, 56 patients with stage IB‐IIB cervical cancer are included in 2 research centers from the discovery cohort. Patient‐specific somatic mutations led to NACT non‐responsiveness are identified by whole‐exome sequencing. Next, CRISPR/Cas9‐based library screenings are performed based on these genes to confirm their biological contribution to drug resistance. A 15‐gene classifier is developed by generalized linear regression analysis combined with the logistic regression model. In an independent validation cohort of 102 patients, the classifier showed good predictive ability with an area under the curve of 0.80 (95% confidence interval (CI), 0.69–0.91). Furthermore, the 15‐gene classifier is significantly associated with patient responsiveness to NACT in both univariate (odds ratio, 10.8; 95% CI, 3.55–32.86; p = 2.8 × 10−5) and multivariate analysis (odds ratio, 17.34; 95% CI, 4.04–74.40; p = 1.23 × 10−4) in the validation set. In conclusion, the 15‐gene classifier can accurately predict the clinical response to NACT before treatment, representing a promising approach for guiding the selection of appropriate treatment strategies for locally advanced cervical cancer.

Objective: 1q44 microdeletion syndrome is difficult to diagnose due to the wide phenotypic spectrum and strong genetic heterogeneity. We explore the correlation between the chromosome microdeletions and phenotype in a child with 1q44 microdeletion syndrome, we collected the clinical features of the patient and combined them with adjacent copy number variation (CNV) regions previously reported.Methods: We collected the full medical history of the patient and summarized her clinical symptoms. Whole-exome sequencing (WES) and CapCNV analysis were performed with DNA extracted from both the patient's and her parents' peripheral blood samples. Fluorescent quantitative PCR (q-PCR) was performed for the use of verification to the CNV regions.Results: A 28.7 KB microdeletion was detected in the 1q44 region by whole-exome sequencing and low-depth whole-genome sequencing. The deleted region included the genes COX20 and HNRNPU. As verification, karyotype analysis showed no abnormality, and the results of qPCR were consistent with that of whole-exome sequencing and CapCNV analysis.Conclusion: The patient was diagnosed with 1q44 microdeletion syndrome with clinical and genetic analysis. Analyzing both whole-exome sequencing and CapCNV analysis can not only improve the diagnostic rate of clinically suspected syndromes that present with intellectual disability (ID) and multiple malformations but also support further study of the correlation between CNVs and clinical phenotypes. This study lays the foundation for the further study of the pathogenesis of complex diseases.

Objective: 1q44 microdeletion syndrome is difficult to diagnose due to the wide phenotypic spectrum and strong genetic heterogeneity. We explore the correlation between the chromosome microdeletions and phenotype in a child with 1q44 microdeletion syndrome, we collected the clinical features of the patient and combined them with adjacent copy number variation (CNV) regions previously reported. Methods: We collected the full medical history of the patient and summarized her clinical symptoms. Whole-exome sequencing (WES) and CapCNV analysis were performed with DNA extracted from both the patient's and her parents' peripheral blood samples. Fluorescent quantitative PCR (q-PCR) was performed for the use of verification to the CNV regions. Results: A 28.7 KB microdeletion was detected in the 1q44 region by whole-exome sequencing and low-depth whole-genome sequencing. The deleted region included the genes COX20 and HNRNPU. As verification, karyotype analysis showed no abnormality, and the results of qPCR were consistent with that of whole-exome sequencing and CapCNV analysis. Conclusion: The patient was diagnosed with 1q44 microdeletion syndrome with clinical and genetic analysis. Analyzing both whole-exome sequencing and CapCNV analysis can not only improve the diagnostic rate of clinically suspected syndromes that present with intellectual disability (ID) and multiple malformations but also support further study of the correlation between CNVs and clinical phenotypes. This study lays the foundation for the further study of the pathogenesis of complex diseases. [ABSTRACT FROM AUTHOR]

Neoadjuvant chemotherapy (NACT) remains an attractive alternative for controlling locally advanced cervical cancer. However, approximately 15–34% of women do not respond to induction therapy. To develop a risk stratification tool, 56 patients with stage IB‐IIB cervical cancer are included in 2 research centers from the discovery cohort. Patient‐specific somatic mutations led to NACT non‐responsiveness are identified by whole‐exome sequencing. Next, CRISPR/Cas9‐based library screenings are performed based on these genes to confirm their biological contribution to drug resistance. A 15‐gene classifier is developed by generalized linear regression analysis combined with the logistic regression model. In an independent validation cohort of 102 patients, the classifier showed good predictive ability with an area under the curve of 0.80 (95% confidence interval (CI), 0.69–0.91). Furthermore, the 15‐gene classifier is significantly associated with patient responsiveness to NACT in both univariate (odds ratio, 10.8; 95% CI, 3.55–32.86; p = 2.8 × 10−5) and multivariate analysis (odds ratio, 17.34; 95% CI, 4.04–74.40; p = 1.23 × 10−4) in the validation set. In conclusion, the 15‐gene classifier can accurately predict the clinical response to NACT before treatment, representing a promising approach for guiding the selection of appropriate treatment strategies for locally advanced cervical cancer. [ABSTRACT FROM AUTHOR]

The congenital myasthenia syndromes (CMS) are a group of autosomal recessive or autosomal dominant diseases that affect neuromuscular junctions. CMS caused by AGRN mutations is very uncommon typically characterized by ptosis, mild weakness, and proximal limb weakness. We report the case of an 8-year-old female who exhibited the onset of motor development retardation from infancy and slow progression to proximal muscle weakness. Repeated nerve stimulation at 3 Hz showed a clear decrement with 17%. Whole exon sequencing showed an AGRN gene compound heterozygous mutation (c.5009C >T and c.5078T > C). She was treated with salbutamol but without improvement. Then pseudoephedrine was adapted as a treatment choice and obtained remarkable curative effect. We have summarized and analyzed 12 patients who have been reported in the literature. An early age of onset and muscle weakness in the lower limbs are the main feature of an early AGRN gene mutation. Both types of AGRN-related CMS respond favorably to ephedrine. This is the first report showing that pseudoephedrine is effective as a choice for the treatment of AGRN-related CMS. [ABSTRACT FROM AUTHOR]

Objective To screen out the pathogenic genes of non-syndrome cleft lip with or without cleft palate ( NSCI/P) in nuclear family. Methods Six patients with NSCI/P were selected, and the elbow venous blood was collected from patients and their parents, genomic DNA was extracted, and pathogenic genes of NSCI/P nuclear family were screened by whole exon sequencing (WES). Results Eighteen peripheral blood samples were collected from 6 NSCI/P nuclear families, and a total of 10 candidate genes and 11 mutation sites were obtained through WES. Conclusion The 10 candidate genes and 11 mutation sites obtained in this study may be related to NSCI/P. [ABSTRACT FROM AUTHOR]

Abstract: Angiomyofibroblastoma (AMF) represents a rare, benign mesenchymal tumor with a predilection for the vulvovaginal region, which may be misdiagnosed as aggressive angiomyxoma (AAM). Herein, we report a case of a 20‐year‐old nulliparous Chinese woman with a unique pedunculated and polypoidal mass, which had been developing within the previous 6 months in the left labium majus, exhibiting the AAM clinical impression but diagnosed as AMF. The mass measured 18 × 10 × 6 cm, and contained diffuse ulcerated areas and purulent discharge. A complete excision of the mass was performed. There was no subsequent evidence of recurrence, according to a 13‐month follow‐up. As a rare benign vulvovaginal tumor, AMF can present on patients of an early reproductive age with rapidly growing, polypoidal pattern. The whole exon sequencing analysis revealed the genomic alterations, which may contribute to the occurrence of AMF. [ABSTRACT FROM AUTHOR]

Purpose: Liquid biopsy using digital PCR (dPCR) has been widely used for the screening of ESR1 mutations, since they are frequently identified in the hotspot. However, dPCR is limited to the known mutations. Therefore, we aimed to analyze the utility of next-generation sequencing (NGS) to discover novel ESR1 mutations. Methods: Whole exon sequencing of the ESR1 gene using NGS was performed in 16 primary and 47 recurrent tumor samples and 38 plasma samples from hormone receptor-positive metastatic breast cancer patients. Functional analyses were then performed for the novel mutations we detected. Results: We identified no mutations in primary tumors and six mutations in five recurrent tumors, including three types of known mutations (Y537C, Y537N, and D538G) and two novel mutations (E279V and G557R). We also identified seven mutations in five plasma samples, including three types of known mutations (S463P, Y537S, and D538G) and one mutation not reported in COSMIC database (L536H). All nine patients with ESR1 mutations were treated with aromatase inhibitors (AIs) prior to sampling, and the mutations were frequently detected in patients who received AI treatments in the metastatic setting. Among the three novel mutations (E279V, L536H, and G557R), L536H, but not E279V and G557R, showed ligand-independent activity. All three mutant proteins showed nuclear localization and had no relation with non-genomic ER pathways. Conclusions: Although the molecular mechanisms of the E279V and G557R mutations remain unclear, our data suggest the utility of NGS as a liquid biopsy for metastatic breast cancer patients and the potential to identify novel ESR1 mutations. [ABSTRACT FROM AUTHOR]

Background: Townes-Brocks syndrome (TBS) is a rare autosomal dominant syndrome that is characterized by a triad of imperforate anus, dysplastic ears, and thumb malformations. Heterozygous variants of SALL1 are responsible for this syndrome. Renal structural abnormalities and functional impairments are often reported in TBS patients., Case Summary: We report a case of TBS in a Chinese family. The index patients showed obvious renal atrophy and renal failure. TBS was suggested after a physical examination and pedigree analysis. Whole exome sequencing revealed a heterozygous variant of SALL1 . The variant (NM&#95;001127892 c.1289&#95;c.1290 insC) led to a read-frame shift of the encoded protein, which was confirmed by Sanger sequencing. The variant cosegregated with the phenotype among affected members., Conclusion: A novel variant in SALL1 gene may be the molecular pathogenic basis of this disorder., Competing Interests: Conflict-of-interest statement: The authors have no conflicts of interest to declare., (©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.)

Background: Copy number variation (CNV) has become widely recognized in recent years due to the extensive use of gene screening in developmental disorders and epilepsy research. 1q21.1 microduplication syndrome is a rare CNV disease that can manifest as multiple congenital developmental disorders, autism spectrum disorders, congenital malformations, and congenital heart defects with genetic heterogeneity., Case Summary: We reported a pediatric patient with 1q21.1 microduplication syndrome, and carried out a literature review to determine the correlation between 1q21.1 microduplication and its phenotypes. We summarized the patient's medical history and clinical symptoms, and extracted genomic DNA from the patient, her parents, elder brother, and sister. The patient was an 8-mo-old girl who was hospitalized for recurrent convulsions over a 2-mo period. Whole exon sequencing and whole genome low-depth sequencing (CNV-seq) were then performed. Whole exon sequencing detected a 1.58-Mb duplication in the CHR1:145883867-147465312 region, which was located in the 1q21.1 region. Family analysis showed that the pathogenetic duplication fragment, which was also detected in her elder brother's DNA originated from the mother., Conclusion: Whole exon sequencing combined with quantitative polymerase chain reaction can provide an accurate molecular diagnosis in children with 1q21.1 microduplication syndrome, which is of great significance for genetic counseling and early intervention., Competing Interests: Conflict-of-interest statement: All the authors have no financial relationship with any commercial entity with a potential interest in the subject of this manuscript., (©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.)

Drug discovery involves various steps and is a long process being even more demanding for complex diseases such as cancer. Tumors are ensembles of subpopulations with different mutations, require very specific and effective strategies. Conventional drug screening technologies may not be adequate and efficient anymore. Drug repositioning is a useful strategy to identify new uses for previously failed drugs. High throughput and deep sequencing technologies provide valuable support by yielding enormous amounts of '-omics' data and contribute to understanding the molecular mechanisms responsible for drug action. Computational methods coupled with systems biology represent a promising step to interpret pharmacogenomic data and establish strong connections with drug discovery. Genomic variations have been found to be linked with differential drug response among individuals. Large genome wide association studies are necessary to identify reliable connections between genomic variations and drug response since personalized medicine has been accepted as an important phenomenon in the drug discovery and development process post approval. [ABSTRACT FROM AUTHOR]

Papillary renal neoplasm with reverse polarity (PRNRP) is a newly defined entity with distinct histomorphology and recurrent KRAS mutation. In this study, we aimed to identify and analyze the clinicopathological, immunohistochemical (IHC), and molecular features of PRNRP in our center and to evaluate its differential diagnosis with other tumors with which it is easily confused: clear cell papillary renal cell carcinoma (CCPRCC), oncocytic papillary renal cell carcinoma (OPRCC), and papillary renal cell carcinoma type 1 (PRCC1). Nephrectomy specimens of PRNRP (n = 15), CCPRCC (n = 11), and OPRCC (n = 12) were retrieved from our pathology archives. We also selected typical cases of PRCC1 (n = 15) as a control group. PRNRP accounted for 3.05% (15/492) of all PRCC cases at our center. The median follow-up period was 41.3 months. All PRNRP cases were pT1N0M0, and only one involved recurrence (1 year after surgery). IHC analysis showed diffuse staining of CK7, EMA, and GATA3 but weak or negative staining of CD10, CD117, p504s, and vimentin in the PRNRP samples and distinctive IHC features in the other three tumor types. KRAS mutation was detected in 4/10 PRNRP cases. Among the 40 most commonly mutated genes identified, 5 (BCLAF1, PDE4DIP, NCOR1, PARP4, and PABPC1) have actionable alterations. Our study supports the suggestion that PRNRP is an entity distinct from CCPRCC, OPRCC, and PRCC1., (Copyright © 2022. Published by Elsevier Inc.)

Knobloch syndrome is an inherited disorder characterized by high myopia, retinal detachment, and occipital defects. Disease-causing mutations have been identified in the COL18A1 gene. This study aimed to investigate novel variants of COL18A1 in Knobloch syndrome and describe the associated phenotypes in Chinese patients. We reported six patients with Knobloch syndrome from four unrelated families in whom we identified five novel COL18A1 mutations. Clinical examination showed that all probands presented with high myopia, chorioretinal atrophy, and macular defects; one exhibited rhegmatogenous retinal detachment in one eye. Occipital defects were detected in one patient. [ABSTRACT FROM AUTHOR]

Background: Neonatal sclerosing cholangitis (NSC) is a severe cholestatic liver disease, which often develops into end-stage liver disease in childhood and requires liver transplantation. Mutations in CLDN1 and DCDC2 are confirmed to be the main pathogenic mechanism of NSC., Methods: Whole exon sequencing (WES) was performed to find the possible disease-causing mutations of this family. The mutation was confirmed by Sanger sequencing, and large fragment copy number variation was confirmed by qPCR., Results: We found novel biallelic mutations c.[705-2A>G];[923&#95;1023del] in the DCDC2 gene of the proband. The proband's father had the heterozygous mutation c.705-2A>G, and his mother had a heterozygous c.923&#95;1023del. The proband's younger brother, who had similar clinical manifestations, was found the same biallelic mutations with the proband., Conclusion: Novel biallelic mutations were identified in DCDC2 of this Chinese family, according to the American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation of sequence variants, both mutations were classified as pathogenic, which might be the cause of NSC in this family., (Copyright © 2020 Elsevier Masson SAS. All rights reserved.)

Objective: To explore the genetic characteristics in a Chinese family with autosomal dominant lateral temporal lobe epilepsy (ADLTE) and analyze the correlation between genotype and phenotype. Methods: The natural history, clinical data and peripheral blood sample were collected in all patients and two healthy members of this ADLTE family. Whole exon sequence (WES) analysis strategy was used to explore the underlying mutations. Possible causative genetic variation was further confirmed by direct PCR and Sanger sequencing. The genotype-phenotype features were compared with previously reported cases. Results: A novel pathogenetic LGI1 frameshift mutation p.T134fs was identified in this study. The clinical phenotype was different from reported. Conclusion: This study reports a pathogenic LGI1 mutation in a Chinese ADLTE family for the first time, which suggests that LGI1 is a new genetic abnormality of ADLTE in Chinese.