Assessing concordance among human, in silico predictions and functional assays on genetic variant classification.

MOTIVATION: A variety of in silico tools have been developed and frequently used to aid high-throughput rapid variant classification, but their performances vary, and their ability to classify variants of uncertain significance were not systemically assessed previously due to lack of validation data. This has been changed recently by advances of functional assays, where functional impact of genetic changes can be measured in single-nucleotide resolution using saturation genome editing (SGE) assay. RESULTS: We demonstrated the neural network model AIVAR (Artificial Intelligent VARiant classifier) was highly comparable to human experts on multiple verified datasets. Although highly accurate on known variants, AIVAR together with CADD and PhyloP showed non-significant concordance with SGE function scores. Moreover, our results indicated that neural network model trained from functional assay data may not produce accurate prediction on known variants. AVAILABILITY AND IMPLEMENTATION: All source code of AIVAR is deposited and freely available at https://github.com/TopGene/AIvar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BRCA germline mutations in an unselected nationwide cohort of Chinese patients with ovarian cancer and healthy controls.

OBJECTIVE: To investigate the BRCA status in Chinese patients with ovarian cancer (OC). Though there were two large prevalence studies in Chinese OC patients, this was the first time to observe it in healthy controls. METHODS: We performed BRCA mutation screening using next-generation sequencing to determine the prevalence of BRCA germline deleterious mutations in an unselected cohort of Chinese OC patients (n = 1331) versus healthy controls (n = 1763) and describe the types and spectrum of BRCA deleterious variants. RESULTS: Among the 1331 patients with OC, 227 (17.1%) carried deleterious variants in BRCA1 and 70 (5.3%) carried deleterious variants in BRCA2. Of 1763 control subjects, 6 (0.3%) and 2 (0.1%) had deleterious variants in BRCA1 and BRCA2. No patient carried mutations in both BRCA1 and BRCA2 simultaneously. Sixty-three novel mutations were identified, and three Chinese specific hot-spot mutations were notified as BRCA1 c.5470_5477delATTGGGCA, BRCA1 c.981_982delAT, and BRCA1 c.3770_3771delAG. Interestingly, all these high-frequency recurrent mutations were distributed on exon 10, which may also be the Chinese OC BRCA mutations' distinct characteristics. In addition, in our study, the estimated odds ratio (OR) of OC associated with BRCA1 positive variants were approximately 34.6 (95% CI, 12.5-95.7) in age group under 40 and 42.4 (95% CI, 5.9-305.2) in group older than 50 in the Chinese population, respectively. CONCLUSIONS: We recommend BRCA testing to all Chinese OC patients and those general Chinese who have family members with hereditary breast and ovarian related cancer (HBOC)-related cancers. Variants carriers would not only benefit from early prevention of OC but also for the medical management.

Assessing the Variations in Breast/Ovarian Cancer Risk for Chinese BRCA1/2 Carriers.

Background: Cancer risks vary in different BRCA1/2 mutations. We are interested in identifying regions associated with elevated/reduced risks of breast/ovarian cancers in the Chinese population and comparing with previously reported Caucasian-based breast/ovarian cancer cluster regions (OCCR/BCCR). We also aim to characterize the distribution and estimate the cancer risks of different Chinese recurrent mutations. Methods: A total of 3,641 cancer-free women and 4,278 female cancer patients were included in the study. Germline BRCA1/2 status was detected with amplicon-based next-generation sequencing. We calculated the odds ratio (OR) of breast cancer and OR of ovarian cancer, and their ratio of the two ORs (ROR) for each region. ROR >1 indicated elevated odds of breast cancer and/or decreasing odds of ovarian cancer, and vice versa. The frequency, distribution, and penetrance of six known Chinese founder mutations were characterized, respectively. Haplotype analysis and age estimation were performed on the most prevalent founder mutation BRCA1: c.5470_5477del. Results: A total of 729 subjects were detected with germline BRCA1/2 deleterious mutations. The putative Chinese OCCR/BCCR partially overlapped with Caucasian-based OCCR/BCCR and shared structural-functional characteristics. The six known Chinese founder mutations greatly vary in both distribution and penetrance. The two widely spread mutations are estimated to convey low penetrance, while the area-restricted founder mutations seemed to confer higher/complete penetrance. BRCA1: c.5470_5477del is estimated to have emerged ∼2,090 years ago (70 B.C.) during the Han dynasty. Conclusions: BRCA1/2 carriers with different genotypes have significantly different cancer risks. An optimal risk assessment should be mutation specific, rather than concerning a single figure.

Retrospective reinterpretation and reclassification of BRCA1/2 variants from Chinese population.

BACKGROUND: The accurate interpretation of BRCA1/2 variants becomes increasingly important in breast cancer and other related cancers including ovarian cancer, prostate cancer, pancreatic cancer and so forth. In the past decades, especially before year 2015, limitations of techniques and lack of databases and guidelines have led to possible misinterpretation of the clinical significance of sequence variants of BRCA1/2. A published study reported reclassification of some BRCA1/2 variants previously classified as variants of uncertain significance (VUS) to likely pathogenic in breast or ovarian cancer patients from Korea. However, little is known about the situation in Chinese population. METHODS: We retrospectively retrieved 109 publications studying about BRCA1/2 variants of Chinese population from the year 1999 to year 2019 (March). After excluding publications of meta-analysis and publications with missing data, 72 publications were eventually retained for subsequent analysis. In total, 1,351 BRCA variants (673 BRCA1 variants and 678 BRCA2 variants) derived from 42,430 Chinese cancer patients were standardized and reinterpreted using ACMG/AMP 2015 guidelines and China Expert Consensus on BRCA variant interpretation by genetic counselors. RESULTS: Among the 1,351 BRCA variants, the majority of interpretation (91.7%, 1,239/1,351) remained the same as previously published. However, there were 112 (8.3%, 112/1,351) variants (64 BRCA1, 48 BRCA2) reclassified with different categories. CONCLUSIONS: Our results demonstrated that clinical significance of not only VUS, but also pathogenic/likely pathogenic variants varied from time to time in the Chinese population. Precise reinterpretation of BRCA1/2 variants is of crucial importance to genetic counseling or clinical decision-making for risk individuals or patients.

OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.

Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology's Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences.