A genome-wide SNP kit for ancient human population genetics

Reduce the cost of sequencing ancient human DNA by orders of magnitude using our myBaits® Expert Human Affinities kit. Starting with a core 1.2M SNPs from the “Boston 1240K” legacy design, the Human Affinities collection also includes an optional 0.9 M additional Y and autosomal SNPs for improved inferences in African and other populations.

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Overview

This bait set targeting more than two million human genomic SNP sites polymorphic in modern and ancient human populations was selected by leaders in ancient human population genetics from the University of Adelaide, Francis Crick Institute, and Harvard Medical School. Its dedicated protocol is tailored for use with degraded or ancient DNA libraries of any type.

Modular structure—For maximum utility, four distinct modules are available in three configuration options:

Prime 1240K: The same sites as the Harvard/Boston 1240K legacy targets.
Ancestral 850K: Sites ascertained using archaic Homo as an outgroup.
Y chromosome 46K: Sites for patrilineal ancestry inquiry.
MitoTrio: Probes tiled across modern human and neanderthal mitogenomes.

Convenient kits—Each myBaits kit includes probes and hybridization/washing reagents.

This myBaits kit can be easily integrated into your own research workflows—or paired with our customizable Sequencing or Bioinformatics services for a seamless NGS solution. Want data faster? The laboratory services team at Daicel Arbor Biosciences has extensive experience working with ancient DNA samples and are ready to help with your project.

Please note that this product will be discontinued at the end of 2023. You can find more details here: December 2023 discontinuation of kit

myBaits kits are for research use only and are not validated for diagnostic or therapeutic purposes.

Performance

In test captures of several ancient human DNA samples, the HA kit retrieved more than 1.6 million sites and achieved high specificity.

To evaluate behavior of the assay, we enriched 17 ancient human Illumina sequencing libraries built from either dsDNA- or ssDNA and one modern human genomic DNA sample. Following sequencing to roughly 30 million read-pairs per library on a Novaseq S4 flowcell, data was aligned to GRCh37/hg19 reference genome and covered SNP sites were tabulated following procedures described by Wang et al. 2019 (Nature Communications).

Reliable recovery of millions of informative SNPs +

Over 1.6 million targeted sites show evidence for enrichment in trial captures. Data shown are the number of targeted sites enriched in any sample for an evaluation panel of 18 human libraries (17 ancient, 1 modern).

Module	Total	Transitions	Transversions
Prime	1,027,178	793,601	233,577
Ancestral	619,079	0	619,079
Y Chromosome	38,369	24,117	14,252

Compatible with ancient DNA libraries with a variety of preservation levels

Data shown for 4 ancient DNA samples with a range of ages and endogenous DNA amounts. SNPs were called from 30 million read-pairs per library following enrichment with the myBaits Expert Human Affinities Complete panel.

Approximate age (YBP)	Geographic origin	Reads on-target (SNPs) after enrichment	Target SNPs covered
8,000	Africa	47.3%	916,221
6,000	Iberia	46.6%	1,007,370
3,000	Levant	31.8%	690,307
3,000	Mesoamerica	10.7%	163,206

No substantial reference sequence bias at putative heterozygous sites

Data shown for a range of ancient and modern test samples with >1000 putative heterozygous sites at a minimum 10X unique read coverage. SNP call and filtering parameters follow Günther & Nettelblad 2019 (PLoS Genetics).