Improved pairwise kinship analysis using massively parallel sequencing |
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| Affiliation: | 1. Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People’s Republic of China;2. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People’s Republic of China;3. Forensic Science Center of Foshan Municipal Public Security Department, Foshan 528000, Guangdong, People’s Republic of China;1. Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden;2. Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden;3. Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain;1. Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China;2. State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, PR China;3. Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, PR China;4. Department of Forensic Genetics, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China;1. Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA;2. Department of Chemistry Malaysia Kuching, Ministry of Science, Technology and Innovation (MOSTI) Malaysia;3. Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia;1. Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria;2. Forensic Science Program, The Pennsylvania State University, PA, USA;1. Department of Forensic Medicine, Criminal Investigation Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang 110854, Liaoning, PR China;2. Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang 110032, Liaoning, PR China |
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| Abstract: | In the present study, 67 individuals from two families were analyzed to explore the efficacy of the ForenSeq™ DNA Signature Prep Kit for pairwise kinship analysis. Six types of pairwise relationships including 81 parent-offspring, 60 full siblings, 48 grandparent-grandchildren, 147 uncle/aunt-nephew/nieces, 97 first cousins and 190 non-relatives were generated from these two families and the corresponding likelihood ratio (LR) was calculated using either sequence-based or length-based STR genotype data (i.e., LRsequence and LRlength). In addition, 10,000 pairs of different relationships were simulated to estimate the system powers of the STRs and SNPs in this panel. The results showed that 54, 9 and 5 additional alleles were observed based on sequence for 27 autosomal STRs, 24 Y-STRs and 7 X-STRs, respectively, compared to those based on length information and 11 novel alleles were identified. Five mutations were found for 58 STRs in 81 parent-offspring but no mutations were observed for SNPs. For 27 autosomal STR loci, the LRs were increased from 9.20, 7.87, 2.01, 2.07, 0.42 for log10LRlength to 11.52, 10.12, 2.61, 2.60, 0.52 for log10LRsequence for paternity index (PI), full siblings index (FSI), grandparent-grandchild index (GI), uncle/aunt-nephew/niece index (UNI) and first cousins index (FCI), respectively. PI values for 94 SNPs separated more than those of 27 STRs if two individuals were non parent-offspring relatives. For the simulation study, the effectiveness was 1 for the parent-offspring relationship at the thresholds of t1 = − 4 and t2 = 4 and was 0.9998 for full siblings (t1 = − 2, t2 = 2). With an error rate of 0.42%, 93.02% of second degree relatives could be identified at the thresholds of t1 = − 1 and t2 = 1. However, the effectiveness was only 0.4300 for first cousins with a relatively high error rate of 2.68% (t1 = − 1, t2 = 1). In conclusion, STR typing according to the sequence information is more polymorphic, which increases the discrimination power for kinship testing. Compared to these 27 STR markers, 94 SNP markers in this panel have advantages in paternity testing especially when mutated STRs are involved or when a relative is an alleged parent. This panel is powerful enough to resolve paternity and full sibling testing. Most of the second degree relationships could be identified with low error rate while more markers are still needed for first cousins testing. |
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| Keywords: | Kinship analysis ForenSeq™ DNA signature prep kit Massively parallel sequencing (MPS) Short tandem repeat (STR) Single nucleotide polymorphism (SNP) |
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