[job] Bioinformatic Scientist, Technology Development at @nygenome https://jobs.silkroad.com/NYGenome/Careers/jobs/696
Nicolas Robine
@robine
- 493 Followers
- 299 Following
- 28 Posts
@notsojunkdna on the bird site, cancer genomics at New York Genome Center. French/US
bioRxivThe Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution https://www.biorxiv.org/content/10.1101/2023.05.07.538753v1?med=mas
Genetic variants in African‑American and Hispanic patients with breast cancer
https://www.spandidos-publications.com/10.3892/ol.2022.13637
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https://www.spandidos-publications.com/10.3892/ol.2022.13637
#p1000Biblio
Genetic variants in African‑American and Hispanic patients with breast cancer
Breast cancer is a disease with significant health disparity affecting mortality in minority women. The present study examined the genetic makeup of breast cancers in African‑American and Hispanic/Latinx patients to determine specific genetic mutations associated with breast cancer in the minority population from South Los Angeles, United States. Whole‑exome sequencing was performed on DNA extracted from breast cancer tumor biopsies collected from 13 African‑American and 15 Hispanic women and 8 matched‑normal samples for each ethnic category. The results were analyzed using Ensemble Variant Effect Predictor and Mutation Significance. Additionally, a comparative analysis with The Cancer Genome Atlas data was provided. Our data revealed somatic mutations in genes such as SET domain containing (lysine methyltransferase) 8, serine protease 1 and AT‑rich interaction domain 1B (<em>ARID1B</em>) and known breast cancer genes, such as <em>BRCA1/2</em>, <em>TP53</em> and the DNA damage response genes across all ethnicities. Additionally, Hispanic patients had BRCA1 associated RING domain 1B (<em>BARD1</em>) variants, while African‑American patients had higher numbers of nonsynonymous variants in the RAD51 paralog B (<em>RAD51B</em>), <em>ARID1B</em> and X‑ray repair cross complementing 3 (<em>XRCC3</em>) genes. In addition, our patients exhibited mutational signature enrichment that indicated DNA homologous recombination repair deficiencies. Therefore, African‑American and Hispanic breast cancer samples showed considerable overlap in breast cancer genetic mutations. However, there are differences in specific genetic variants in <em>TP53</em>, <em>BRCA1/2,</em> <em>BARD1</em> or <em>ARID1B</em>, which will require further study of their role in tumorigenesis.
Jonathan PritchardHere's a slightly updated version for people who asked for a pdf
Link to pdf version: https://www.dropbox.com/s/pqer35laylxejl0/Intro-KeyNumbers-printalone.pdf?dl=0
Matthew HerperMadrigal experimental drug delivers strong results in fatty liver disease known as NASH
My story on today's positive results. Much better than people were expecting.
Racial/ethnic and sex differences in somatic cancer gene mutations among patients with early-onset colorectal cancer
https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-22-0764/711679/Racial-ethnic-and-sex-differences-in-somatic
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https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-22-0764/711679/Racial-ethnic-and-sex-differences-in-somatic
#p1000Biblio
Racial/ethnic and sex differences in somatic cancer gene mutations among patients with early-onset colorectal cancer
Abstract. Molecular features underlying colorectal cancer (CRC) disparities remain uncharacterized. Here, we investigated somatic mutation patterns by race/ethnicity and sex among 5,856 non-Hispanic White (NHW), 535 non-Hispanic Black (NHB) and 512 Asian/Pacific Islander (API) CRC patients[2,016 early-onset:sequencing age<50]. NHB patients with early-onset non-hypermutated CRC, but not API patients, had higher adjusted tumor mutation rates than NHW patients. There were significant differences for LRP1B, FLT4, FBXW7, RNF43, ATRX, APC and PIK3CA mutation frequencies in early-onset non-hypermutated CRCs between racial/ethnic groups. Heterogeneities by race/ethnicity were observed for the effect of APC, FLT4 and FAT1 between early-onset and late-onset non-hypermutated CRC. By sex, heterogeneity was observed for the effect of EP300, BRAF, WRN, KRAS, AXIN2 and SMAD2. Males and females with non-hypermutated CRC had different trends in EP300 mutations by age group. These findings define genomic patterns of early-onset non-hypermutated CRC by race/ethnicity and sex, which yields novel biological clues into early-onset CRC disparities.
Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria
https://www.biorxiv.org/content/10.1101/2022.12.09.519178v1?ct=
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My kid’s school must be wondering why all French kids have a dentist’s appointment tomorrow at 2pm 😂😂😂 #FRAMOR #WorldCup2022 #AllezLesBleus
Integrated analysis of racial disparities in genomic architecture identifies a transancestry prognostic subtype in bladder cancer
https://febs.onlinelibrary.wiley.com/doi/abs/10.1002/1878-0261.13360
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https://febs.onlinelibrary.wiley.com/doi/abs/10.1002/1878-0261.13360
#p1000Biblio
PRState: Incorporating genetic ancestry in prostate cancer risk scores for men of African ancestry
https://bmccancer.biomedcentral.com/articles/10.1186/s12885-022-10258-3
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https://bmccancer.biomedcentral.com/articles/10.1186/s12885-022-10258-3
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PRState: Incorporating genetic ancestry in prostate cancer risk scores for men of African ancestry - BMC Cancer
Background Prostate cancer (PrCa) is one of the most genetically driven solid cancers with heritability estimates as high as 57%. Men of African ancestry are at an increased risk of PrCa; however, current polygenic risk score (PRS) models are based on European ancestry groups and may not be broadly applicable. The objective of this study was to construct an African ancestry-specific PrCa PRS (PRState) and evaluate its performance. Methods African ancestry group of 4,533 individuals in ELLIPSE consortium was used for discovery of African ancestry-specific PrCa SNPs. PRState was constructed as weighted sum of genotypes and effect sizes from genome-wide association study (GWAS) of PrCa in African ancestry group. Performance was evaluated using ROC-AUC analysis. Results We identified African ancestry-specific PrCa risk loci on chromosomes 3, 8, and 11 and constructed a polygenic risk score (PRS) from 10 African ancestry-specific PrCa risk SNPs, achieving an AUC of 0.61 [0.60–0.63] and 0.65 [0.64–0.67], when combined with age and family history. Performance dropped significantly when using ancestry-mismatched PRS models but remained comparable when using trans-ancestry models. Importantly, we validated the PRState score in the Million Veteran Program (MVP), demonstrating improved prediction of PrCa and metastatic PrCa in individuals of African ancestry. Conclusions African ancestry-specific PRState improves PrCa prediction in African ancestry groups in ELLIPSE consortium and MVP. This study underscores the need for inclusion of individuals of African ancestry in gene variant discovery to optimize PRSs and identifies African ancestry-specific variants for use in future studies.