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Sasako T, Ilboudo Y, Liang KYH, Chen Y, Yoshiji S, Richards JB. The influence of trinucleotide repeats in the androgen receptor gene on androgen-related traits and diseases. J Clin Endocrinol Metab 2024:dgae302. [PMID: 38701087 DOI: 10.1210/clinem/dgae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/05/2024]
Abstract
CONTEXT Trinucleotide repeats in the androgen receptor have been proposed to influence testosterone signaling in men, but the clinical relevance of these trinucleotide repeats remains controversial. OBJECTIVE To examine how androgen receptor trinucleotide repeat lengths affect androgen-related traits and disease risks and whether they influence the clinical importance of circulating testosterone levels. METHODS We quantified CAG and GGC repeat lengths in the androgen receptor (AR) gene of European-ancestry male participants in UK Biobank from whole-genome and whole-exome sequence data using ExpansionHunter, and tested associations with androgen-related traits and diseases. We also examined whether the associations between testosterone levels and these outcomes were affected by adjustment for the repeat lengths. RESULTS We successfully quantified the repeat lengths from whole-genome and/or whole-exome sequence data in 181,217 males. Both repeat lengths were shown to be positively associated with circulating total testosterone level and bone mineral density, whereas CAG repeat length was negatively associated with male-pattern baldness, but their effects were relatively small and were not associated with most of the other outcomes. Circulating total testosterone level was associated with various outcomes, but this relationship was not affected by adjustment for the repeat lengths. CONCLUSION In this large-scale study, we found that longer CAG and GGC repeats in the AR gene influence androgen resistance, elevate circulating testosterone level via a feedback loop and play a role in some androgen-targeted tissues. Generally, however, circulating testosterone level is a more important determinant of androgen action in males than repeat lengths.
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Affiliation(s)
- Takayoshi Sasako
- McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Tanaka Diabetes Clinic Omiya, Saitama, Japan
| | - Yann Ilboudo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Kevin Y H Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Québec, Canada
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Five Prime Sciences Inc, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King's College London, London, UK
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Voicu AA, Krützen M, Bilgin Sonay T. Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution. FRONTIERS IN BIOINFORMATICS 2021; 1:695784. [PMID: 36303734 PMCID: PMC9581056 DOI: 10.3389/fbinf.2021.695784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
The genus Pongo is ideal to study population genetics adaptation, given its remarkable phenotypic divergence and the highly contrasting environmental conditions it’s been exposed to. Studying its genetic variation bears the promise to reveal a motion picture of these great apes’ evolutionary and adaptive history, and also helps us expand our knowledge of the patterns of adaptation and evolution. In this work, we advance the understanding of the genetic variation among wild orangutans through a genome-wide study of short tandem repeats (STRs). Their elevated mutation rate makes STRs ideal markers for the study of recent evolution within a given population. Current technological and algorithmic advances have rendered their sequencing and discovery more accurate, therefore their potential can be finally leveraged in population genetics studies. To study patterns of population variation within the wild orangutan population, we genotyped the short tandem repeats in a population of 21 individuals spanning four Sumatran and Bornean (sub-) species and eight Southeast Asian regions. We studied the impact of sequencing depth on our ability to genotype STRs and found that the STR copy number changes function as a powerful marker, correctly capturing the demographic history of these populations, even the divergences as recent as 10 Kya. Moreover, gene ontology enrichments for genes close to STR variants are aligned with local adaptations in the two islands. Coupled with more advanced STR-compatible population models, and selection tests, genomic studies based on STRs will be able to reduce the gap caused by the missing heritability for species with recent adaptations.
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Affiliation(s)
| | - Michael Krützen
- Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Tugce Bilgin Sonay
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
- *Correspondence: Tugce Bilgin Sonay,
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Rajan-Babu IS, Peng JJ, Chiu R, Li C, Mohajeri A, Dolzhenko E, Eberle MA, Birol I, Friedman JM. Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions. Genome Med 2021; 13:126. [PMID: 34372915 PMCID: PMC8351082 DOI: 10.1186/s13073-021-00932-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/05/2021] [Indexed: 02/01/2023] Open
Abstract
Background Screening for short tandem repeat (STR) expansions in next-generation sequencing data can enable diagnosis, optimal clinical management/treatment, and accurate genetic counseling of patients with repeat expansion disorders. We aimed to develop an efficient computational workflow for reliable detection of STR expansions in next-generation sequencing data and demonstrate its clinical utility. Methods We characterized the performance of eight STR analysis methods (lobSTR, HipSTR, RepeatSeq, ExpansionHunter, TREDPARSE, GangSTR, STRetch, and exSTRa) on next-generation sequencing datasets of samples with known disease-causing full-mutation STR expansions and genomes simulated to harbor repeat expansions at selected loci and optimized their sensitivity. We then used a machine learning decision tree classifier to identify an optimal combination of methods for full-mutation detection. In Burrows-Wheeler Aligner (BWA)-aligned genomes, the ensemble approach of using ExpansionHunter, STRetch, and exSTRa performed the best (precision = 82%, recall = 100%, F1-score = 90%). We applied this pipeline to screen 301 families of children with suspected genetic disorders. Results We identified 10 individuals with full-mutations in the AR, ATXN1, ATXN8, DMPK, FXN, or HTT disease STR locus in the analyzed families. Additional candidates identified in our analysis include two probands with borderline ATXN2 expansions between the established repeat size range for reduced-penetrance and full-penetrance full-mutation and seven individuals with FMR1 CGG repeats in the intermediate/premutation repeat size range. In 67 probands with a prior negative clinical PCR test for the FMR1, FXN, or DMPK disease STR locus, or the spinocerebellar ataxia disease STR panel, our pipeline did not falsely identify aberrant expansion. We performed clinical PCR tests on seven (out of 10) full-mutation samples identified by our pipeline and confirmed the expansion status in all, showing absolute concordance between our bioinformatics and molecular findings. Conclusions We have successfully demonstrated the application of a well-optimized bioinformatics pipeline that promotes the utility of genome-wide sequencing as a first-tier screening test to detect expansions of known disease STRs. Interrogating clinical next-generation sequencing data for pathogenic STR expansions using our ensemble pipeline can improve diagnostic yield and enhance clinical outcomes for patients with repeat expansion disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00932-9.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada. .,Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK.
| | - Junran J Peng
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada
| | | | | | - Chenkai Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Arezoo Mohajeri
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
| | | | | | - Inanc Birol
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
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