Chromosome 3 Deletion

High-throughput sequencing of core STR loci for forensic genetic ...

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.

The analysis of short tandem repeat (STR) loci is an important tool in forensic genetics. Currently, STRs are mostly typed by DNA fragment analysis using PCR-based forensic STR kits and multicolor fluorescence capillary electrophoresis (CE) ( 1 ). Generally, the majority of STRs routinely investigated in forensic genetics are correlated to a well-defined allelic ladder repeat number. However, occasional variant or ‘off-ladder’ alleles are observed ( 2 - 6 ). Current methods, although fast and cost-effective, do not allow full resolution of the STR loci. Recently, researchers have used pyrosequencing ( 7 ) or electrospray ionization mass spectrometry (ESI-MS) ( 8 , 9 ) to identify variants within or near repeat regions. However, with the ESI-MS method, only the base pair composition is obtained, and although variations compared with a reference sequence can be detected, variant positions cannot be determined. While a pyrosequencing approach was used to analyze STR loci in a low-throughput application ( 7 ), this methodology does not allow for the deep sequence coverage provided by high-throughput sequencing.

Since its inception in 2005, so-called high-throughput sequencing has become a rapid and reliable tool for massively parallel sequencing ( 10 ). The Roche FLX Genome Sequencer (GS FLX) system (and its related model, the GS Junior; both from Roche Applied Science, Indianapolis, IN, USA) is a pyrosequencing platform that can sequence hundreds of samples in parallel through the use of sample-specific multiple identifier (MID) tags. High-quality sequence reads of 400 bp or longer are routinely obtained, and the use of emulsion-PCR allows sequencing of one single bead-bound fragment within its own microreactor. Thus, the entire sequence of an STR allele can be obtained in a single experiment without confusion from competing reactions (e.g., from the allele on the other chromosome). While the GS FLX has proven to have some difficulties in accurately sequencing homopolymers ( 10 ), to date there has been no investigation into the sequencing of repeat regions using this technology for human DNA profiling. Until now, high-throughput sequencing has only been used for STR studies involving ancient DNA from extinct moas and for microsatellite location for species identification ( 11 - 14 ). These studies, however, used de novo sequencing to locate STRs rather than investigating well-defined STR regions.

Chromosome 3q29 deletion with gastrointestinal malformation: a case

A micturating cysto-urethrogram confirmed the common channel of the deformity. Ultrasonography of the abdomen was normal. Skeletal survey and brain magnetic resonance imaging results were normal. A chromosomal analysis was carried out, involving 20 CTG-banded cells from two cultures, and five cells were karotyped and photographed, showing 46,XX,del(3)(q29) (Figure 2 ).

Catalogue of unbalanced chromosome aberrations in man

Mendelian inheritance in man, a catalog of human genes and genetic disorders

NORD guide to rare disorders

Rubin's Pathology, clinicopathologic foundations of medicine

Chromosome 3 deletion mapping in human small cell lung cancer