HID-Ion AmpliSeq™ Identity Panel

Catalog number: A25643

Applied Biosystems™  Related applications: DNA Sequencing | Ion Torrent™ Next-Generation Sequencing | Sample Prep⁄Extraction for Human Identification

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Description

The HID-Ion AmpliSeq™ Identity Panel is one of the first next-generation sequencing solutions for human identification that uniquely identifies pristine or degraded samples. The multiplexed panel of SNPs provides discrimination of individuals similar to STR genotype match probabilities used by forensic analysts (between 1x10-31 and 6x10-35). This pre-designed, ready-to-use panel version follows up on a previous HID-Ion AmpliSeq™ Identity community panel.

High discrimination power is achieved by using 34 upper Y-Clade SNPs and 90 autosomal SNPs that have high heterozygosity and low fixation index (Fst) as described in publications by Dr. Kenneth Kidd from Yale University and the SNPForID Consortium (1-3). The panel design has been optimized for use with degraded or challenging forensic samples using only 1 ng of starting DNA input, although acceptable performance has been observed with sub-nanogram input quantities as low as 180 pg. The autosomal markers have an average amplicon length of 132 nucleotides and the Y-markers are 141 nucleotides in length on average.

A concordance study was conducted with 30 control samples for the 46 SNPs discovered by Dr. Kidd, using input amounts as low as 180 pg and as high as 1 ng of gDNA. The 30 samples were analyzed on one run of the Ion PGM™ sequencer using an Ion 318™ chip (V2.0). The sequenced reads were analyzed using Variant Caller 4.0 software followed by the HID SNP Genotyper plug-in, both on the Torrent Suite Server. Results from the study demonstrate a concordance rate of 99.99% for the 46 SNPs, at an average read depth of ~750x per autosomal SNP and ~350x per Y-SNP.

Recommended Configuration
Samples per chip: 8 per Ion 314™ chip, 38 per Ion 316™ chip, 77 per Ion 318™ chip (assuming 80% loading and 60% usable reads)
Minimum coverage: for 97% of autosomal SNPs to have >300x, an average of 738x should be targeted. For 97% of Y-SNPs to have >150x, an average coverage of 236x should be targeted. This corresponds to ~75k reads per individual.

References:
1. Pakstis, A. J., Speed, W. C., Fang, R., Hyland, F. C., Furtado, M. R., Kidd, J. R., & Kidd, K. K. (2010). SNPs for a universal individual identification panel. Human Genetics, 127(3), 315-324.
2. Phillips, C., Fang, R., Ballard, D., Fondevila, M., Harrison, C., Hyland, F., et al. (2007). Evaluation of the Genplex SNP typing system and a 49plex forensic marker panel. Forensic Science International: Genetics, 1(2), 180-185.
3. Karafet, T. M., Mendez, F. L., Meilerman, M. B., Underhill, P. A., Zegura, S. L., & Hammer, M. F. (2008). New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Research, 18(5), 830-838.
For Research, Forensic, or Paternity Use Only. Not for use in diagnostic procedures.

Specifications

For Use With (Equipment): Ion PGM™ System
Library Type: Targeted Sequencing Library
Workflow Step: Library Generation
Starting Material: DNA
Sequencing Type: Genome & DNA Sequencing
Product Size: 96 reactions
Final Product: PCR Amplicons

Contents & storage

Store in freezer (-5 to -30°C).

Documents

Manuals & protocols