HKG: an open genetic variant database of 205 Hong Kong cantonese exomes

Understanding the genetic epidemiology of hereditary breast cancer in India using whole genome data from 1029 healthy individuals

Breast cancer is the most highly reported cancer in India. Genetic testing could help tackle the increasing cancer burden by enabling carriers obtain early diagnosis through increased surveillance, and help guide treatment. However, accurate interpretation of variant pathogenicity must be established in a population-specific manner to ensure effective use of genetic testing. Here we query IndiGen data obtained from sequencing 1029 Indian individuals, and perform variant classification of all reported BRCA variants using gold-standard ACMG & AMP guidelines to establish disease epidemiology. To address the high number of VUS variants thus obtained, we further utilize the brca-NOVUS ML tool to obtain pathogenicity predictions in a manner close to ACMG guidelines at scale. Through the manual application of ACMG & AMP guidelines, we determined the genetic prevalence to be the following: 1 in 342 carriers of BRCA1, and 1 in 256 carriers of BRCA2 pathogenic/likely pathogenic variants bear a significant lifetime risk of developing breast / ovarian cancer in India. The high population prevalence and unique variant landscape emphasizes a need for population-scale studies of causative variants to enable effective screening. We advise cautious clinical interpretation, given incomplete penetrance and other complex factors that result in cancer disease. To the best of our knowledge, this is the first and most comprehensive population-scale genetic epidemiological study of BRCA-linked breast cancer variants reported from India.

Understanding the variant landscape, and genetic epidemiology of Multiple Endocrine Neoplasia in India

PURPOSE

Multiple Endocrine Neoplasia (MEN) is a group of familial cancer syndromes that encompasses several types of endocrine tumors differentiated by genetic mutations in RET, MEN1 and CDKN1B genes. Accurate diagnosis of MEN subtypes can thus be performed through genetic testing. However, MEN variants remain largely understudied in Indian populations. Additionally, few dedicated resources to understand these disorders currently exist.

METHODS

Using the gold-standard ACMG/AMP guidelines, we systematically classified variants reported across the three genes in the IndiGen dataset, and established the genetic epidemiology of MEN in the Indian population. We further classified ClinVar and Mastermind variants and compiled all into a database. Finally, we designed a multiplex primer panel for rapid variant identification.

RESULTS

We have established the genetic prevalence of MEN as the following: 1 in 1026 individuals is likely to be afflicted with MEN linked with pathogenic RET mutations. We have further created the MAPVar database containing 3280 ACMG-classified variants freely accessible at: https://clingen.igib.res.in/MAPVar/ . Finally, our NGS primer panel covers 33 exonic regions across two pools through 38 amplicons with a total amplified region of 65 kb.

CONCLUSION

Our work establishes that MEN is a prevalent disorder in India. The rare nature of Indian variants underscores the need of genomic and functional studies to establish a more comprehensive variant landscape. Additionally, our panel offers a means of cost-effective genetic testing, and the MAPVar database a ready reference to aid in a better understanding of variant pathogenicity in clinical as well as research settings.