Pairwise kinship analysis of 17 pedigrees using massively parallel sequencing

Ruiyang Tao; Qiannan Xu; Shouyu Wang; Ruocheng Xia; Qi Yang; Anqi Chen; Yiling Qu; Yehui Lv; Suhua Zhang; Chengtao Li

doi:10.1016/j.fsigen.2021.102647

Pairwise kinship analysis of 17 pedigrees using massively parallel sequencing

Forensic Sci Int Genet. 2022 Mar:57:102647. doi: 10.1016/j.fsigen.2021.102647. Epub 2021 Dec 1.

Authors

Ruiyang Tao¹, Qiannan Xu², Shouyu Wang³, Ruocheng Xia¹, Qi Yang¹, Anqi Chen⁴, Yiling Qu⁵, Yehui Lv⁶, Suhua Zhang⁷, Chengtao Li⁸

Affiliations

¹ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China.
² Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China.
³ Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, PR China.
⁴ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, PR China.
⁵ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China.
⁶ Shanghai University of Medicine & Health Sciences, Shanghai 200237, PR China.
⁷ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China. Electronic address: zhangsh@ssfjd.cn.
⁸ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China. Electronic address: lichengtaohla@163.com.

PMID: 34902810
DOI: 10.1016/j.fsigen.2021.102647

Abstract

With the tremendous development of massively parallel sequencing (MPS) in the last decade, it has been widely applied in basic science, clinical diagnostics, microbial genomics, as well as forensic genetics. MPS has lots of advantages that may facilitate the kinship analysis. In this study, 243 Chinese Han individuals from 17 families were involved and sequenced using the ForenSeq™ DNA Signature Prep Kit (Verogen, Inc., San Diego, USA), which provided the sequence information of 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative SNPs (iSNPs). A total of 275 pairs of parent-child, 123 pairs of full siblings, 1 pair of twins, 1 pair of half siblings, 158 pairs of grandparent-grandchild, 222 pairs of uncle/aunt-nephew/niece and 121 pairs of first cousins, as well as 701 pairs of unrelated individuals were identified. Using both likelihood ratio (LR) and identical by state (IBS) methods, the kinship analysis was conducted among these relative and non-relative pairs based on the A-STRs and SNPs. As a result, the ForenSeq Signature Kit could solve the analysis of parent-child (t1 = -4, t2 = 4), full siblings (t1 = -2, t2 = 2) and most second-degree kinships (t1 = -1, t2 = 1) using the LR method. When the IBS method was applied, 123 full sibling pairs had a higher average IBS value than other kinship groups in this study. And the IBS method could play a role in the testing of parent-child and full siblings.

Keywords: Forensic genetics; IBS; Kinship analysis; LR; Massively parallel sequencing (MPS).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Fingerprinting* / methods
Forensic Genetics* / methods
High-Throughput Nucleotide Sequencing
Humans
Microsatellite Repeats*
Pedigree
Polymorphism, Single Nucleotide
Sequence Analysis, DNA