A study led by researchers at the New York Genome Center (NYGC) has achieved the largest-to-date survey of Y Chromosome Short Tandem Repeat (Y-STR) mutation rates, enhancing forensic and genealogy applications as well as a basic understanding of DNA variations.
Dr. Yaniv Erlich, Core Member at NYGC, member of Columbia’s Data Science Institute and Assistant Professor of Computer Science and Computational Biology at Columbia, led the study. The research team consisted of scientists from NYGC, Columbia University, Massachusetts Institute of Technology, Stanford University and the Wellcome Trust Sanger Institute.
The Y chromosome is only found in males and is passed down from father to son. Due to this unique inheritance pattern, Y-STRs are often used in forensics, paternity and genealogical DNA testing to trace paternal lineage (the father of the father of the…). Published in the May 5, 2016 issue of The American Journal of Human Genetics, the study “Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates,characterized about 4,000 Y-STRs and identified about 500 new markers that could be used to further refine parental lines.
STRs are genomic sequences where a small DNA word reoccurs multiple times, such as ACACACAC. These sequences are prone to mutations and span nearly 1% of the human genome. However, the mutation rates of most STRs are unknown due to the narrow bandwidth of technologies traditionally used to probe these sequences. This limitation has precluded forensics and genetic genealogy applications from fully leveraging these sequences.
To obtain these insights, the researchers first developed MUTEA, an algorithm that estimates STR mutation rates from population-scale data. MUTEA uses a high-resolution genealogy inferred from other types of mutations on the Y chromosome. After validating their approach, the researchers used MUTEA to analyze whole-genome sequencing data from more than 1,000 males in the 1000 Genomes Project, resulting in the largest collection of Y-STR mutation rates to date. The 1000 Genomes Project was one of the first large-scale whole genome sequencing projects, providing insights into the scale of human genetic variation. In addition, the study used the Y-STR mutation rates to estimate the number of new STR mutations in the genome in each new offspring, illuminating a hidden layer of genetic variation.
A companion paper on Y chromosome evolution was released in Nature Genetics on April 25, 2016, “Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences,” which also utilized data from the 1000 Genomes Project. In this study, the research team described 1,244 Y chromosome sequences and discovered more than 65,000 variants.
“Together, the two studies show the importance of STRs in understanding how mutations fuel evolutionary processes,” Dr. Erlich said. “Our findings show that the number of new STR mutations are likely to be larger than other types of genetic variations, such as point mutations and chromosomal aberrations.”
About the New York Genome Center
The New York Genome Center (NYGC) is an independent, nonprofit at the forefront of transforming biomedical research and clinical care with the mission of saving lives. As a consortium of renowned academic, medical and industry leaders across the globe, NYGC focuses on translating genomic research into clinical solutions for serious disease. Our member organizations and partners are united in this unprecedented collaboration of technology, science, and medicine. We harness the power of innovation and discoveries to improve people’s lives — ethically, equitably, and urgently. Member institutions include: Albert Einstein College of Medicine, American Museum of Natural History, Cold Spring Harbor Laboratory, Columbia University, Cornell University/Weill Cornell Medicine, Hospital for Special Surgery, The Jackson Laboratory, Memorial Sloan Kettering Cancer Center, Icahn School of Medicine at Mount Sinai, NewYork-Presbyterian Hospital, The New York Stem Cell Foundation, New York University, Northwell Health (formerly North Shore-LIJ), The Rockefeller University, Roswell Park Cancer Institute, Stony Brook University and IBM.
