TY - JOUR
T1 - Linkage and linkage disequilibrium among the markers in the forensic MPS panels
AU - Li, Ran
AU - Budowle, Bruce
AU - Sun, Hongyu
AU - Ge, Jianye
N1 - Funding Information:
This study was funded in part with internal funds of the Center for Human Identification at the University of North Texas Health Science Center, the National Natural Science Foundation of China (81971798), and the Natural Science Foundation of Guangdong Province (2019A15150).
Publisher Copyright:
© 2021 American Academy of Forensic Sciences
PY - 2021/9
Y1 - 2021/9
N2 - For the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium. In this study, publicly accessible genomic data from five representative populations were used to evaluate the genetic linkage and linkage disequilibrium (LD) between autosomal markers represented in six major commercial panels (in total, 362 markers). Among the 3041 syntenic marker pairs, 1524 pairs had sex-average genetic distances <50 cM, and thus, these marker pairs can be considered as genetically linked. Among the 143 marker pairs with physical distances <1 Mb, 19 LD haplotype blocks (comprising 39 SNPs in total) were detected for at least one of the tested populations. Statistical methods for interpreting linked markers and/or markers in LD were suggested for various case scenarios.
AB - For the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium. In this study, publicly accessible genomic data from five representative populations were used to evaluate the genetic linkage and linkage disequilibrium (LD) between autosomal markers represented in six major commercial panels (in total, 362 markers). Among the 3041 syntenic marker pairs, 1524 pairs had sex-average genetic distances <50 cM, and thus, these marker pairs can be considered as genetically linked. Among the 143 marker pairs with physical distances <1 Mb, 19 LD haplotype blocks (comprising 39 SNPs in total) were detected for at least one of the tested populations. Statistical methods for interpreting linked markers and/or markers in LD were suggested for various case scenarios.
KW - evidence interpretation
KW - genetic linkage
KW - haplotype block
KW - linkage disequilibrium
KW - match probability
KW - short tandem repeats
KW - single nucleotide polymorphisms
UR - http://www.scopus.com/inward/record.url?scp=85104643434&partnerID=8YFLogxK
U2 - 10.1111/1556-4029.14724
DO - 10.1111/1556-4029.14724
M3 - Article
C2 - 33885147
AN - SCOPUS:85104643434
VL - 66
SP - 1637
EP - 1646
JO - Journal of forensic sciences
JF - Journal of forensic sciences
SN - 0022-1198
IS - 5
ER -