High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform

TY - JOUR

T1 - High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform

AU - Fordyce, Sarah Louise

AU - Avila Arcos, Maria del Carmen

AU - Rockenbauer, Eszter

AU - Børsting, Claus

AU - Frank-Hansen, Rune

AU - Petersen, Johan Frederik Torp

AU - Willerslev, Eske

AU - Hansen, Anders Johannes

AU - Morling, Niels

AU - Gilbert, Tom

PY - 2011/8/1

Y1 - 2011/8/1

N2 - The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method in combination with a bioinformatic tool designed specifically to analyze sequence lengths and frequencies, we found that GS FLX STR sequence data are comparable to conventional capillary electrophoresis-based STR typing. Furthermore, we found DNA base substitutions and repeat sequence variations that would not have been identified using conventional STR typing.

AB - The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method in combination with a bioinformatic tool designed specifically to analyze sequence lengths and frequencies, we found that GS FLX STR sequence data are comparable to conventional capillary electrophoresis-based STR typing. Furthermore, we found DNA base substitutions and repeat sequence variations that would not have been identified using conventional STR typing.

U2 - 10.2144/000113721

DO - 10.2144/000113721

M3 - Journal article

C2 - 21806557

SN - 0736-6205

VL - 51

SP - 127

EP - 133

JO - BioTechniques

JF - BioTechniques

IS - 2

ER -