Development and Validation of the AmpFℓSTR® Identifiler® Direct PCR Amplification Kit: A Multiplex Assay for the Direct Amplification of Single-Source Samples*,†

Wang, Dennis Y.; Chang, Chien-Wei; Lagacé, Robert; Oldroyd, Nicola J.; Hennessy, Lori K.

doi:10.1111/j.1556-4029.2011.01757.x

Cited by 50 publications

(32 citation statements)

References 16 publications

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“…New CE instrumentation also allowed the concurrent electrophoretic separation of more samples thereby increasing throughput [6,[11][12]. There have also been some attempts toward the direct PCR amplification of samples, thereby bypassing DNA extraction and quantification [6,[13][14][15]. These are, however, attempts which accelerate individual steps of the DNA analysis process.…”

Section: Introductionmentioning

confidence: 97%

Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell ® DNA IQ™/Identifiler ® Plus/ABI 3500xL workflow

Thong

Phua

Loo

et al. 2015

Forensic Science International: Genetics

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Section: Introductionmentioning

confidence: 97%

Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell ® DNA IQ™/Identifiler ® Plus/ABI 3500xL workflow

Thong

Phua

Loo

et al. 2015

Forensic Science International: Genetics

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“…This population was chosen as a relevant, well characterised population group upon which to conduct this concordance study [5,6]. Similar studies have sampled similar numbers of individuals from single [13,14] or multiple ethnic groups [4,8,9] represented within their geographical location. Loci were tested for departures from Hardy Weinberg expectations (HWE) using Genepop software [15,16].…”

Section: Introductionmentioning

confidence: 99%

Concordance study between the ParaDNA ® Intelligence Test, a Rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR ® SGM Plus ® )

Ball

Dawnay

Stafford-Allen

et al. 2015

Forensic Science International: Genetics

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The ParaDNA® Intelligence Test enables STR profiling directly from human biological samples and evidence items collected from crime scene in 75 min. Designed for non-expert use this system allows DNA information to be available to investigators before it would typically be available from a laboratory. The ParaDNA Intelligence Test system amplifies D3S1358, D8S119, D16S539, D18S1358and TH01 STR loci and the gender typing locus amelogenin and detects the alleles present with HyBeacon1 probes. Individual DNA samples from 381 UK Caucasian individuals were analysed using AmpFlSTR1 SGM Plus® and the ParaDNA Intelligence Test with the derived STR profiles compared. Here we describe the high level of concordance demonstrated between the two systems and discuss this with reference to allele frequencies and the discriminatory power offered by the ParaDNA Intelligence Test.

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“…Sequencing library construction frequently includes polymerase chain reaction (PCR) steps during which a polymerase might undergo slippage at STRs, leading to amplicons that differ in length due to expansion and contraction of repeat units (Ellegren 2004;Wang et al 2011). Additionally, base calling by NGS instruments at repetitive regions is frequently imprecise.…”

mentioning

confidence: 99%

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

et al. 2015

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Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCRfree protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution.

show abstract

Development and Validation of the AmpFℓSTR® Identifiler® Direct PCR Amplification Kit: A Multiplex Assay for the Direct Amplification of Single-Source Samples*,†

Cited by 50 publications

References 16 publications

Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell ® DNA IQ™/Identifiler ® Plus/ABI 3500xL workflow

Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell ® DNA IQ™/Identifiler ® Plus/ABI 3500xL workflow

Concordance study between the ParaDNA ® Intelligence Test, a Rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR ® SGM Plus ® )

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

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