Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements

Walther Parson; David Ballard; Bruce Budowle; John M Butler; Katherine B Gettings; Peter Gill; Leonor Gusmão; Douglas R Hares; Jodi A Irwin; Jonathan L King; Peter de Knijff; Niels Morling; Mechthild Prinz; Peter M Schneider; Christophe Van Neste; Sascha Willuweit; Christopher Phillips

doi:10.1016/j.fsigen.2016.01.009

Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements

Forensic Sci Int Genet. 2016 May:22:54-63. doi: 10.1016/j.fsigen.2016.01.009. Epub 2016 Jan 21.

Authors

Walther Parson¹, David Ballard², Bruce Budowle³, John M Butler⁴, Katherine B Gettings⁴, Peter Gill⁵, Leonor Gusmão⁶, Douglas R Hares⁷, Jodi A Irwin⁷, Jonathan L King⁸, Peter de Knijff⁹, Niels Morling¹⁰, Mechthild Prinz¹¹, Peter M Schneider¹², Christophe Van Neste¹³, Sascha Willuweit¹⁴, Christopher Phillips¹⁵

Affiliations

¹ Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA. Electronic address: [email protected].
² Faculty of Life Sciences, King's College, London, UK.
³ Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
⁴ National Institute of Standards and Technology, Gaithersburg, MD, USA.
⁵ Norwegian Institute of Public Health, Department of Forensic Biology, Oslo, Norway; Department of Forensic Medicine, University of Oslo, Oslo, Norway.
⁶ DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Brazil; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal; Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal.
⁷ FBI Laboratory, Quantico, VA, USA.
⁸ Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA.
⁹ Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
¹⁰ Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
¹¹ Department of Sciences, John Jay College for Criminal Justice, New York, NY, USA.
¹² Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne, Germany.
¹³ Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
¹⁴ Institute of Legal Medicine, Humboldt University, Berlin, Germany.
¹⁵ Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.

PMID: 26844919
DOI: 10.1016/j.fsigen.2016.01.009

Abstract

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data.

Keywords: MPS; Massively parallel sequencing; NGS; Next generation sequencing; Nomenclature; STRs; Short tandem repeats.

MeSH terms

DNA / genetics
Databases, Nucleic Acid / standards
Forensic Genetics / methods*
Forensic Genetics / standards*
Genotype
High-Throughput Nucleotide Sequencing / methods*
Humans
Microsatellite Repeats / genetics
Polymorphism, Genetic
Terminology as Topic*

Substances

DNA