Novel mutations in actionable breast cancer genes by targeted sequencing in an ethnically homogenous cohort

Detection of Genetic Variations in Children with Tetralogy of Fallot Using Whole Exome Sequencing Technology Integrated Bioinformatics Analysis

Background: Tetralogy of Fallot (TOF) is the most common cyanotic heart defect in newborns, with a complex etiology and genetic variation considered to be one of the main pathogenic factors. Identifying genetic variations associated with TOF has important clinical value for understanding its pathogenesis, patient susceptibility, and prognosis of patients with TOF. Therefore, this study aimed to identify potential pathogenic genes of TOF through comprehensive genetic analysis. Materials and Methods: In this study, we employed whole exome sequencing (WES) of the DNA of 47 Chinese children who received surgical TOF treatment at the Children's Hospital of Zhejiang University of Medicine and processed for DNA extraction and quantification of the DNA following WES using the Illumina NovaSeq platform. WES data undergo strict quality control and analysis processes including alignment, postprocessing, variant calling, annotation, and prioritization. Key tools, such as GATK's haplotype calling module and Annotate Variation, were used for variant annotation. In addition, by combining bioinformatics tools such as SIFT, Polyphen2, and Clin Pred, we evaluated the potential impact of nonsynonymous mutations on protein function and referred to relevant literature to support our prediction. Results: Comprehensive data analysis and quality assessment analysis corroborated the data generated from the WES dataset of 47 patients with TOF. Interpreting variants from the perspective of clinical pathogenicity results revealed a novel polymorphism and variant associated with TOF. The identified genetic results revealed evidence for a major contribution of MUTYH, RARB, GFM1, PDZD2, CEP57, DCPS, POMT2, BUB1B, CYP19A1, MAZ, USP10, and TCF3 and provided novel findings for functionally interacting proteins associated with the pathomechanism of TOF. Seven pathogenic variants related to TOF were detected, most of which were previously unreported in this cohort. Conclusions: The genetic variations discovered in this study emphasize the importance of genetic factors in the pathogenesis of TOF, revealing its complex molecular pathways and protein-protein interactions. The study of genetic diversity provides a new perspective for understanding the etiology of TOF and promotes an in-depth exploration of its pathological mechanisms. These findings lay the foundation for subsequent clinical research and the development of treatment strategies.

Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort

PURPOSE

The genetic underpinning of neurodevelopmental disorders (NDDs) in diverse ethnic populations, especially those with high rates of consanguinity, remains largely unexplored. Here, we aim to elucidate genomic insight from 576 well-phenotyped and highly consanguineous (16%) NDD cohort.

METHODS

We used chromosomal microarray (CMA; N:247), exome sequencing (ES; N:127), combined CMA and ES (N:202), and long-read genome sequencing to identify genetic etiology. Deep clinical multivariate data were coupled with genomic variants for stratification analysis.

RESULTS

Genetic diagnosis rates were 17% with CMA, 29.92% with ES, and 37.13% with combined CMA and ES. Notably, children of consanguineous parents showed a significantly higher diagnostic yield (P < .01) compared to those from nonconsanguineous parents. Among the ES-identified pathogenic variants, 36.19% (38/105) were novel, implicating 35 unique genes. Long-read sequencing of seizure participants unresolved by combined test identified expanded FMR1 trinucleotide repeats. Additionally, we identified 2 recurrent X-linked variants in the G6PD in 3.65% (12/329) of NDD participants. These variants were absent in large-population control cohorts and cohort comprising neurodevelopmental and neuropsychiatric populations of European descendants, indicating a possible associated risk factor potentially resulting from ancient genetic drift.

CONCLUSION

This study unveils unique clinical and genomic insights from a consanguinity rich Bangladeshi NDD cohort, highlighting a strong association of G6PD with NDD in this population.

Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders

Introduction: Copy number variations (CNVs) play a critical role in the pathogenesis of neurodevelopmental disorders (NDD) among children. In this study, we aim to identify clinically relevant CNVs, genes and their phenotypic characteristics in an ethnically underrepresented homogenous population of Bangladesh. Methods: We have conducted chromosomal microarray analysis (CMA) for 212 NDD patients with male to female ratio of 2.2:1.0 to identify rare CNVs. To identify candidate genes within the rare CNVs, gene constraint metrics [i.e., "Critical-Exon Genes (CEGs)"] were applied to the population data. Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) was followed in a subset of 95 NDD patients to assess the severity of autism and all statistical tests were performed using the R package. Results: Of all the samples assayed, 12.26% (26/212) and 57.08% (121/212) patients carried pathogenic and variant of uncertain significance (VOUS) CNVs, respectively. While 2.83% (6/212) patients' pathogenic CNVs were found to be located in the subtelomeric regions. Further burden test identified females are significant carriers of pathogenic CNVs compared to males (OR = 4.2; p = 0.0007). We have observed an increased number of Loss of heterozygosity (LOH) within cases with 23.85% (26/109) consanguineous parents. Our analyses on imprinting genes show, 36 LOH variants disrupting 69 unique imprinted genes and classified these variants as VOUS. ADOS-2 subset shows severe social communication deficit (p = 0.014) and overall ASD symptoms severity (p = 0.026) among the patients carrying duplication CNV compared to the CNV negative group. Candidate gene analysis identified 153 unique CEGs in pathogenic CNVs and 31 in VOUS. Of the unique genes, 18 genes were found to be in smaller (<1 MB) focal CNVs in our NDD cohort and we identified PSMC3 gene as a strong candidate gene for Autism Spectrum Disorder (ASD). Moreover, we hypothesized that KMT2B gene duplication might be associated with intellectual disability. Conclusion: Our results show the utility of CMA for precise genetic diagnosis and its integration into the diagnosis, therapy and management of NDD patients.

BRCA1/BRCA2 mutation spectrum analysis in South Asia: a systematic review

Objective

Breast cancer (BC) is the most common form of cancer among Asian females. Mutations in the BRCA1/BRCA2 genes are often observed in BC cases and largely increase the lifetime risk of having BC. Because of the paucity of high-quality data on the molecular spectrum of BRCA mutations in South Asian populations, we aimed to explore these mutations among South Asian countries.

Methods

A systematic literature search was performed for the BRCA1 and BRCA2 gene mutation spectrum using electronic databases such as PubMed, EMBASE, and Google Scholar. Twenty studies were selected based on specific inclusion and exclusion criteria.

Results

The 185delAG (c.68_69del) mutation in exon 2 of BRCA1 was the most common recurrent mutation and founder mutation found. Various intronic variants, variants of unknown significance, large genomic rearrangements, and polymorphisms were also described in some studies.

Conclusions

The South Asian population has a wide variety of genetic mutations of BRCA1 and BRCA2 that differ according to countries and ethnicities. A stronger knowledge of various population-specific mutations in these cancer susceptibility genes can help provide efficient strategies for genetic testing.

Molecular Spectra and Frequency Patterns of Somatic Mutations in Arab Women with Breast Cancer

BACKGROUND

The role of somatic mutations in breast cancer prognosis and management continues to be recognized. However, data on the molecular profiles of Arab women are limited.

MATERIALS AND METHODS

This was a cross-sectional study based on medical chart review of all Arab women diagnosed with breast cancer at a single institution between 2010 and 2018 who underwent next-generation sequencing with Ampliseq 46-Gene or 50-Gene.

RESULTS

A total of 78 Arab women were identified, with a median age at diagnosis of 52.3 years (range: 37-82 years; 38.5% ≤50 years). The majority of patients had stage III or IV disease (74.4%). Next-generation sequencing revealed the following somatic mutation rates: TP53, 23.1%; ATM, 2.6%; IDH1, 2.6%; IDH2, 3.8%; PTEN, 7.7%; PIK3CA, 15.4%; APC, 7.7%; NPM1, 2.5%; MPL, 1.3%; JAK2, 2.5%; KIT, 7.7%; KRAS, 3.8%; and NRAS, 3.8%.

CONCLUSION

Our study illustrates frequencies of somatic mutations in Arab women with breast cancer and suggests potential variations from estimates reported in the Western population. These data calls for larger epidemiologic studies considering the evolving role of such mutations in prognostication and personalized management.

Whole exome sequencing uncovered highly penetrant recessive mutations for a spectrum of rare genetic pediatric diseases in Bangladesh

Collectively, rare genetic diseases affect a significant number of individuals worldwide. In this study, we have conducted whole-exome sequencing (WES) and identified underlying pathogenic or likely pathogenic variants in five children with rare genetic diseases. We present evidence for disease-causing autosomal recessive variants in a range of disease-associated genes such as DHH-associated 46,XY gonadal dysgenesis (GD) or 46,XY sex reversal 7, GNPTAB-associated mucolipidosis II alpha/beta (ML II), BBS1-associated Bardet-Biedl Syndrome (BBS), SURF1-associated Leigh Syndrome (LS) and AP4B1-associated spastic paraplegia-47 (SPG47) in unrelated affected members from Bangladesh. Our analysis pipeline detected three homozygous mutations, including a novel c. 863 G > C (p.Pro288Arg) variant in DHH, and two compound heterozygous variants, including two novel variants: c.2972dupT (p.Met991Ilefs*) in GNPTAB and c.229 G > C (p.Gly77Arg) in SURF1. All mutations were validated by Sanger sequencing. Collectively, this study adds to the genetic heterogeneity of rare genetic diseases and is the first report elucidating the genetic profile of (consanguineous and nonconsanguineous) rare genetic diseases in the Bangladesh population.

Identification of Novel BRCA1 and RAD50 Mutations Associated With Breast Cancer Predisposition in Tunisian Patients

Background

Deleterious mutations on BRCA1/2 genes are known to confer high risk of developing breast and ovarian cancers. The identification of these mutations not only helped in selecting high risk individuals that need appropriate prevention approaches but also led to the development of the PARP-inhibitors targeted therapy. This study aims to assess the prevalence of the most frequent BRCA1 mutation in Tunisia, c.211dupA, and provide evidence of its common origin as well as its clinicopathological characteristics. We also aimed to identify additional actionable variants using classical and next generation sequencing technologies (NGS) which would allow to implement cost-effective genetic testing in limited resource countries.

Patients and Methods

Using sanger sequencing, 112 breast cancer families were screened for c.211dupA. A set of patients that do not carry this mutation were investigated using NGS. Haplotype analysis was performed to assess the founder effect and to estimate the age of this mutation. Correlations between genetic and clinical data were also performed.

Results

The c.211dupA mutation was identified in 8 carriers and a novel private BRCA1 mutation, c.2418dupA, was identified in one carrier. Both mutations are likely specific to North-Eastern Tunisia. Haplotype analysis supported the founder effect of c.211dupA and showed its recent origin. Phenotype-genotype correlation showed that both BRCA1 mutations seem to be associated with a severe phenotype. Whole Exome Sequencing (WES) analysis of a BRCA negative family revealed a Variant of Unknown Significance, c.3647C > G on RAD50. Molecular modeling showed that this variant could be classified as deleterious as it is responsible for destabilizing the RAD50 protein structure. Variant prioritization and pathway analysis of the WES data showed additional interesting candidate genes including MITF and ANKS6.

Conclusion

We recommend the prioritization of BRCA1-c.211dupA screening in high risk breast cancer families originating from the North-East of Tunisia. We also highlighted the importance of NGS in detecting novel mutations, such as RAD50-c.3647C > G. In addition, we strongly recommend using data from different ethnic groups to review the pathogenicity of this variant and reconsider its classification in ClinVar.