{"id":10266,"date":"2017-03-13T20:01:36","date_gmt":"2017-03-13T20:01:36","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=10266"},"modified":"2018-05-24T03:21:42","modified_gmt":"2018-05-24T03:21:42","slug":"can-ancestry-snps-generate-investigative-leads","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/can-ancestry-snps-generate-investigative-leads\/","title":{"rendered":"Can Ancestry SNPs Generate Investigative Leads?"},"content":{"rendered":"

You have a crime scene sample, extracted plenty of DNA, and searched the sample profile against your national DNA database \u2013 you\u2019ve received no hits\u2026 nothing at all. For many casework labs, the lack of a match is potentially a stopping point in the investigation. Now what\u2019s the next step? First, let\u2019s think about AIMs. Ancestry Informative Markers<\/a> are SNPs that are scattered across the genome with different frequencies among various populations1<\/sup> and can be used to assess the biogeographic origins of an individual. Add to that the ability to multiplex and analyze hundreds of such SNPs in a single reaction using massively parallel sequencing (MPS). Now forensic DNA analysts have an avenue for generating investigative leads for their law enforcement partners.<\/p>\n\n\n\n
The Applied Biosystems\u2122 Precision ID Ancestry Panel<\/a> includes 165 autosomal markers that provide biogeographic ancestry information. Fifty-five of these markers were selected based on a publication by Dr. Kenneth Kidd2<\/sup> , and 123 markers were selected based on a publication by Dr. Michael Seldin3<\/sup>. These amplicons are all <130 bases in length which makes them ideal for analyzing degraded samples. Let\u2019s take a look at how this approach is being used to evaluate samples and populations from around the globe.<\/td>\n\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

mtDNA + Y-STRs + piSNPs + AIMs = Biogeographical Ancestry of a Carbonized Corpse<\/strong><\/h4>\n

\"\"An unidentified adult male body was found in Paris (2014) but no further information could be determined. There were no matching dental records, an STR profile did not generate a match to any database and all personal belongings found were charred. The French authorities then approved the use of additional genetic analyses. Hollard, C., et al devised a strategy to analyze mtDNA for maternal lineage, Y-STRs for paternal lineage, AIMs for additional elucidation of biogeographic ancestry and phenotypic SNPs for physical traits.<\/a> The combined results from all these tests indicated an individual from either the Mediterranean Basin or Southwest Asia. The mtDNA haplotype from EMPOP was HV0, found primarily in west Eurasian populations, the Y-STR profile was E1b1b with a match in 2 Tunisian individuals, piSNP showed a 95% chance of having brown eyes, and AIMs results from Precision ID Ancestry Panel and HID SNP Genotyper<\/a> showed ancestry from southwest Asia and Mediterranean regions. The admixture analysis from the two subpanels showed slightly different results, likely due to the available underlying populations. According to the authors \u201c\u2026this work has already provided elements that are useful to the progress of the investigation and it also highlighted specific issues that will arise in concrete forensic cases4<\/sup>.<\/p>\n

First Step for Using Ancestry Inference in Crime Labs<\/strong><\/h4>\n

\"\"The Section of Forensic Genetics at the University of Copenhagen recently published their validation of identity SNP usage in their crime laboratory<\/a>. They\u2019ve now begun to establish the parameters needed to use ancestry SNPs as well. In Pereira,V et al<\/a>, the team has evaluated parameters such as locus balance, heterozygote balance and noise level in the Precision ID Ancestry Panel<\/a> and set their analysis criteria accordingly. In this study, the team analyzed DNA from 142 subjects of Danish ancestry, 98 individuals from Somalia and included data from a previous study of 77 individuals from Greenland<\/a>5<\/sup>. They include a material and methods section that describes their changes to standard protocol and describe why they have chosen to eliminate 3 SNPs from the final analysis. This study stresses the importance of using suitable reference populations to infer ancestry, particularly populations with admixture6<\/sup>.<\/p>\n

Custom Panel Design Tailored to Your Regional Needs<\/strong><\/h4>\n

\"\"The EUROFORGEN consortium has designed a new global ancestry informative SNP panel using the Ion AmpliSeq\u2122 design<\/a> pipeline. Eduardoff, M. et al originally designed a panel consisting of 128 SNPs, of which 125 performed well for a first-time conversion rate of 97.6%.<\/a> For the three SNP assays that underperformed, two of them were replaced with new assays. After evaluation of the primers, the group recommends pre-selection of markers that avoid homopolymer content and indels in the flanking sequence as a key to success. In this study, the group tested inter-laboratory performance across five sites that included sequencing performance on the Ion PGM\u2122 System<\/a>, sensitivity analysis via serial dilution and use of degraded DNA samples, and mixture detection. The results for the 14 study populations, across the five major continental populations, showed very good results for group differentiation and admixture detection. However south Asian populations were not well discriminated and additional markers specific to those populations are being sourced7<\/sup>.<\/p>\n

More and more labs are investigating how they can implement targeted sequencing of ancestry informative SNPs using MPS to help solve more crimes. Whether it\u2019s an off-the-shelf panel<\/a> or one designed especially for your geographic region<\/a>, the Precision ID NGS System for human identification<\/a> offers flexibility and simplicity for your applications. Dr. Soizic Le-Gunier from IGNA in France has discussed how SNP genotyping will have an impact in the future<\/a>.<\/p>\n

To keep up-to-date on all the latest news from the human identification team, from CE to NGS, you can subscribe to our blog<\/a> and quarterly newsletter<\/a>, and follow us on Facebook<\/a> and Twitter<\/a>.<\/p>\n

References:<\/p>\n

    \n
  1. Bruce Budowle and Angela van Daal. Forensically relevant SNP classes<\/a>. BioTechniques 44:603-610 (25th Anniversary Issue, April 2008)<\/li>\n
  2. Kidd, K et al. Better SNPs for Better Forensics: Ancestry, Phenotype, and Family Identification<\/a>. Poster presented at the National Institute of Justice (NIJ) annual meeting, Arlington VA, June 2012.<\/li>\n
  3. Kosoy R, Nassir R, Tian C, et al. (2009) Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America<\/a>.\u00a0Hum Mutat<\/em>\u00a030(1):69\u201378<\/li>\n
  4. Hollard, C. et al. Case report: on the use of the HID-Ion AmpliSeq\u2122 Ancestry Panel in a real forensic case International Journal of Legal Medicine<\/a>. March 2017,Volume 131,\u00a0Issue\u00a02,\u00a0pp 351-358.<\/li>\n
  5. Espregueira Themudo, Gon\u00e7alo et al. Frequencies of HID-ion ampliseq ancestry panel markers among Greenlanders Forensic Science International: Genetics<\/a>, Volume 24 , 60 – 64<\/li>\n
  6. Pereira,V., et al. Evaluation of the Precision ID Ancestry Panel for crime case work: a SNP typing assay developed for typing of 165 ancestral informative markers<\/a>, Forensic Science International: Genetics<\/li>\n
  7. Eduardoff, M. et al Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM\u2122 Forensic Science International<\/a>: Genetics , Volume 23 , 178 \u2013 189<\/li>\n<\/ol>\n

    For Research, Forensic or Paternity Use Only. Not for use in diagnostic procedures.<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

    You have a crime scene sample, extracted plenty of DNA, and searched the sample profile against your national DNA database \u2013 you\u2019ve received no hits\u2026 nothing at all. For many casework labs, the lack of a match is potentially a stopping point in the investigation. Now what\u2019s the next step? First, let\u2019s think about AIMs.<\/p>\n","protected":false},"author":115,"featured_media":10277,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[71],"tags":[153,11,74,156],"division":[],"class_list":{"0":"post-10266","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-forensics","8":"tag-genomic-variants","9":"tag-ion-torrent","10":"tag-sequencing","11":"tag-targeted-dna-sequencing","12":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nCan Ancestry SNPs Generate Investigative Leads? - Behind the Bench<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/can-ancestry-snps-generate-investigative-leads\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Can Ancestry SNPs Generate Investigative Leads?\" \/>\n<meta property=\"og:description\" content=\"You have a crime scene sample, extracted plenty of DNA, and searched the sample profile against your national DNA database \u2013 you\u2019ve received no hits\u2026 nothing at all. 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applications ranging from plasmid verification to confirming next-generation sequencing results. Yet as research evolves, so do the demands placed on sequencing workflows. Today\u2019s labs are not only looking for accuracy\u2014they need speed, flexibility, and reliable\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"DNA sequencing sample tube with DNA helix and sequencing chromatogram representing Sanger sequencing workflow.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":20004,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/a-guide-to-nucleic-acid-quality-control-dna-and-rna-purity\/","url_meta":{"origin":10266,"position":1},"title":"A Guide to Nucleic Acid Quality Control: DNA and RNA Purity","author":"Marlene Gasdia-Cochrane","date":"September 22, 2026","format":false,"excerpt":"Article Summary Nucleic acid quality control helps researchers evaluate DNA and RNA concentration and purity before downstream applications such as PCR, qPCR, and next-generation sequencing (NGS). A standardized workflow combining reliable extraction, concentration and purity assessment, application-appropriate quantification, and consistent laboratory practices can help identify sample issues early, improve reproducibility,\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Close-up shot of a dna sequence on a screen, a digital representation of genetic code, used for analysis.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19168,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/understanding-dna-melting-analysis-using-uv-visible-spectroscopy\/","url_meta":{"origin":10266,"position":2},"title":"Understanding DNA Melting Analysis Using UV-Visible Spectroscopy","author":"Marlene Gasdia-Cochrane","date":"October 14, 2025","format":false,"excerpt":"DNA melting analysis is a vital molecular biology technique used to study the stability and properties of DNA by monitoring its transition from double-stranded to single-stranded form with increasing temperature. UV-visible spectroscopy measures changes in DNA absorbance during this process, providing insights into DNA stability, sequence composition, and molecular interactions.\u2026","rel":"","context":"In "Pharma & Biotech Manufacturing"","block_context":{"text":"Pharma & Biotech Manufacturing","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/pharmamfg\/"},"img":{"alt_text":"Close-up Of Dna Molecule On Blue Background","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19883,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/building-a-better-sample-qc-workflow-from-extraction-to-sequencing\/","url_meta":{"origin":10266,"position":3},"title":"Building a Better Sample QC Workflow: From Extraction to Sequencing","author":"Marlene Gasdia-Cochrane","date":"August 25, 2026","format":false,"excerpt":"Article Summary Successful genomics experiments don't begin with sequencing\u2014they begin with sample quality. Every downstream application, from PCR to next-generation sequencing (NGS), depends on starting with nucleic acids that are accurately quantified and free from contaminants that could compromise results. Establishing a consistent quality control workflow helps laboratories improve reproducibility\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"A pipette drops a liquid into a petri dish with a dna sequence background, science concept. It suggests medical or genetic research.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19943,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/dna-and-rna-purity-ratios-a260-a280-and-a260-a230-explained\/","url_meta":{"origin":10266,"position":4},"title":"DNA and RNA Purity Ratios: A260\/A280 and A260\/A230 Explained","author":"Marlene Gasdia-Cochrane","date":"September 1, 2026","format":false,"excerpt":"Overview DNA and RNA purity ratios help researchers assess nucleic acid sample quality before downstream analysis. The A260\/A280 ratio can indicate potential protein contamination, while the A260\/A230 ratio can reveal residual salts, phenol, guanidine compounds, and other extraction-related contaminants. For a more complete assessment, purity ratios should be evaluated alongside\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"mRNA Technology - Messenger RNA - Two Strands of mRNA on Abstract Technology Background - Development of New Therapies and Vaccines Based on mRNA Technology - Conceptual Illustration","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-1366552805_mrna.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-1366552805_mrna.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-1366552805_mrna.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-1366552805_mrna.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-1366552805_mrna.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-1366552805_mrna.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19447,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/philadelphia-chromosome-like-all-digital-pcr\/","url_meta":{"origin":10266,"position":5},"title":"Unlocking Cancer\u2019s Genetic Secrets with Digital PCR","author":"Behind The Bench Staff","date":"February 27, 2026","format":false,"excerpt":"In this episode of Absolute Gene-ius, we explore how digital PCR (dPCR) is transforming leukemia research with Valeria Rangel, a PhD candidate at the University of California, Irvine. Her work focuses on Philadelphia chromosome-like (Ph-like) B-cell acute lymphoblastic leukemia (ALL), a rare, aggressive subtype that disproportionately affects Hispanic populations. 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