Tags

Type your tag names separated by a space and hit enter

Comparison of CE- and MPS-based analyses of forensic markers in a single cell after whole genome amplification.
Forensic Sci Int Genet. 2020 03; 45:102211.FS

Abstract

Whole genome amplification (WGA) allows for multiple genetic analyses with low template DNA, such as DNA derived from a single cell. WGA could increase the amount of input DNA from the pg to the μg level. However, there are no studies comparing the performance of forensic markers with DNA from a single cell after WGA evaluated on both capillary electrophoresis (CE) and massively parallel sequencing (MPS) platforms. In this study, cell lines consisting of female cultured B-lymphoblastoid cells and karyocytes from male venous blood were segregated into one, two, three and five cells. Including the references with the bulk cells, all samples were generated by WGA with the multiple displacement amplification (MDA) strategy in triplicate and genotyped on CE and MPS platforms. Allele balance, stutter ratio, accuracy, repeatability and concordance of short tandem repeat (STR) markers were used to evaluate the genotyping performance on both platforms. Additionally, the sequence coverage ratio (SCR) and SNP genotypes were evaluated for sequence information generated from the MPS. Heterozygous loci showed high allele balance, with an overall average allele balance ratio larger than 0.79 on the CE and 0.75 on the MPS platforms for the venous blood cell samples; the cultured B-lymphoblastoid cell samples had ratios of 0.62 and 0.70, respectively. The stutter ratio of every source and cell number from both cell line samples were very close, ranging from 5.3%-7.2% for autosomal STRs and approximately 10 % of Y chromosomal STRs on the CE platform. The average stutter, allele, and sequence-based and length-based noise ratios were 6.6 %, 88 %, 4.7 % and 0.7 %, respectively, in the single male cell sample. SNPs also showed high consistency and intralocus balance. Our study indicated that WGA with MDA strategy works relatively well of STR and SNP genotyping with low copy number samples on CE and MPS, even with one-cell sample.

Authors+Show Affiliations

University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.Beijing Huayan Judicial Authentication Institute, Beijing 100192, PR China.CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.Shanxi Medical University, Taiyuan 030009, PR China.Shanxi Medical University, Taiyuan 030009, PR China.Shanxi Medical University, Taiyuan 030009, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China. Electronic address: yanjw@sxmu.edu.cn.

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

31812097

Citation

Chen, Man, et al. "Comparison of CE- and MPS-based Analyses of Forensic Markers in a Single Cell After Whole Genome Amplification." Forensic Science International. Genetics, vol. 45, 2020, p. 102211.
Chen M, Zhang J, Zhao J, et al. Comparison of CE- and MPS-based analyses of forensic markers in a single cell after whole genome amplification. Forensic Sci Int Genet. 2020;45:102211.
Chen, M., Zhang, J., Zhao, J., Chen, T., Liu, Z., Cheng, F., Fan, Q., & Yan, J. (2020). Comparison of CE- and MPS-based analyses of forensic markers in a single cell after whole genome amplification. Forensic Science International. Genetics, 45, 102211. https://doi.org/10.1016/j.fsigen.2019.102211
Chen M, et al. Comparison of CE- and MPS-based Analyses of Forensic Markers in a Single Cell After Whole Genome Amplification. Forensic Sci Int Genet. 2020;45:102211. PubMed PMID: 31812097.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparison of CE- and MPS-based analyses of forensic markers in a single cell after whole genome amplification. AU - Chen,Man, AU - Zhang,Jingjing, AU - Zhao,Jing, AU - Chen,Tong, AU - Liu,Zhiyong, AU - Cheng,Feng, AU - Fan,Qingwei, AU - Yan,Jiangwei, Y1 - 2019/11/29/ PY - 2019/06/17/received PY - 2019/11/11/revised PY - 2019/11/25/accepted PY - 2019/12/8/pubmed PY - 2021/2/2/medline PY - 2019/12/8/entrez KW - Capillary electrophoresis KW - Forensic loci KW - Low copy number KW - Massively parallel sequencing KW - Whole genome amplification SP - 102211 EP - 102211 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 45 N2 - Whole genome amplification (WGA) allows for multiple genetic analyses with low template DNA, such as DNA derived from a single cell. WGA could increase the amount of input DNA from the pg to the μg level. However, there are no studies comparing the performance of forensic markers with DNA from a single cell after WGA evaluated on both capillary electrophoresis (CE) and massively parallel sequencing (MPS) platforms. In this study, cell lines consisting of female cultured B-lymphoblastoid cells and karyocytes from male venous blood were segregated into one, two, three and five cells. Including the references with the bulk cells, all samples were generated by WGA with the multiple displacement amplification (MDA) strategy in triplicate and genotyped on CE and MPS platforms. Allele balance, stutter ratio, accuracy, repeatability and concordance of short tandem repeat (STR) markers were used to evaluate the genotyping performance on both platforms. Additionally, the sequence coverage ratio (SCR) and SNP genotypes were evaluated for sequence information generated from the MPS. Heterozygous loci showed high allele balance, with an overall average allele balance ratio larger than 0.79 on the CE and 0.75 on the MPS platforms for the venous blood cell samples; the cultured B-lymphoblastoid cell samples had ratios of 0.62 and 0.70, respectively. The stutter ratio of every source and cell number from both cell line samples were very close, ranging from 5.3%-7.2% for autosomal STRs and approximately 10 % of Y chromosomal STRs on the CE platform. The average stutter, allele, and sequence-based and length-based noise ratios were 6.6 %, 88 %, 4.7 % and 0.7 %, respectively, in the single male cell sample. SNPs also showed high consistency and intralocus balance. Our study indicated that WGA with MDA strategy works relatively well of STR and SNP genotyping with low copy number samples on CE and MPS, even with one-cell sample. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/31812097/Comparison_of_CE__and_MPS_based_analyses_of_forensic_markers_in_a_single_cell_after_whole_genome_amplification_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(19)30285-6 DB - PRIME DP - Unbound Medicine ER -