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Filipino DNA variation at 12 X-chromosome short tandem repeat markers.
Forensic Sci Int Genet. 2018 09; 36:e8-e12.FS

Abstract

Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq™ DNA Signature Prep kit of the MiSeq® FGx™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications.

Authors+Show Affiliations

DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Philippine Genome Center, University of the Philippines, Philippines. Electronic address: jmsalvador@up.edu.ph.Philippine Genome Center, University of the Philippines, Philippines.DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Philippine Genome Center, University of the Philippines, Philippines.DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Philippine Genome Center, University of the Philippines, Philippines.DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Philippine Genome Center, University of the Philippines, Philippines; Balik Scientist, Philippine Council for Industry, Energy and Emerging Technology Research and Development - Department of Science and Technology, Philippines.DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Philippine Genome Center, University of the Philippines, Philippines.

Pub Type(s)

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

Language

eng

PubMed ID

29909139

Citation

Salvador, Jazelyn M., et al. "Filipino DNA Variation at 12 X-chromosome Short Tandem Repeat Markers." Forensic Science International. Genetics, vol. 36, 2018, pp. e8-e12.
Salvador JM, Apaga DLT, Delfin FC, et al. Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Sci Int Genet. 2018;36:e8-e12.
Salvador, J. M., Apaga, D. L. T., Delfin, F. C., Calacal, G. C., Dennis, S. E., & De Ungria, M. C. A. (2018). Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Science International. Genetics, 36, e8-e12. https://doi.org/10.1016/j.fsigen.2018.06.008
Salvador JM, et al. Filipino DNA Variation at 12 X-chromosome Short Tandem Repeat Markers. Forensic Sci Int Genet. 2018;36:e8-e12. PubMed PMID: 29909139.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Filipino DNA variation at 12 X-chromosome short tandem repeat markers. AU - Salvador,Jazelyn M, AU - Apaga,Dame Loveliness T, AU - Delfin,Frederick C, AU - Calacal,Gayvelline C, AU - Dennis,Sheila Estacio, AU - De Ungria,Maria Corazon A, Y1 - 2018/06/08/ PY - 2018/01/29/received PY - 2018/06/06/revised PY - 2018/06/07/accepted PY - 2018/6/18/pubmed PY - 2018/12/12/medline PY - 2018/6/18/entrez KW - Filipino KW - Genotyping KW - Massively parallel sequencing KW - Population genetics KW - X-STR SP - e8 EP - e12 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 36 N2 - Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq™ DNA Signature Prep kit of the MiSeq® FGx™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/29909139/Filipino_DNA_variation_at_12_X_chromosome_short_tandem_repeat_markers_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(18)30049-8 DB - PRIME DP - Unbound Medicine ER -