myBaits Expert — Predesigned Panels
myBaits Expert Human Affinities
Capture expert-curated population-informative SNPs from any human sample, including ancient and degraded DNA.

The Daicel Arbor Biosciences myBaits Expert Human Affinities Kit is the latest addition to our targeted sequencing portfolio for human population genomics research. Designed and tested in collaboration with leaders in ancient human population genetics, the kit contains hybridization capture probes and reagents that target more than 2 million sites in the human genome known to be polymorphic in living and ancient world populations.

  • Designed and tested in collaboration with leading researchers
  • Probes targeting >2 million sites polymorphic in human populations
  • Compatible with virtually any NGS library from human degraded DNA samples

This kit saves the population genetics researcher orders of magnitude in sequencing and analysis costs compared to total genomic DNA sequencing, particularly for degraded samples with low endogenous human DNA content. It pairs seamlessly with virtually all library preparation chemistries and sequencing platforms. The Human Affinities panel is provided as a complete in-solution target capture kit including buffers, blockers, and probes, along with an easy-to-use protocol.

Want data quickly? Our myReads® NGS services team can perform NGS library preparation, target capture, sequencing, and bioinformatics analysis for projects of any size. Our team of scientists offers decades of collective experience working with challenging samples, including ancient DNA. Contact our experts today to design a targeted ancient DNA NGS project that aligns with your budget and project goals.

Ordering Information
Size
Cat#
Qty
Price
myBaits Expert Human Affinities Kit – Complete
Kit for capturing SNPs from human ancient DNA samples. "Complete" target set includes 4 premixed probeset modules: Prime 1240K, Ancestral 850K, Y Chr 46K, and MitoTrio. Each myBaits kit reaction is sufficient to enrich 1 sample.
351016
$4,780
myBaits Expert Human Affinities Kit – Prime Plus
Kit for capturing SNPs from human ancient DNA samples. "Prime Plus" target set includes 3 premixed probeset modules: Prime 1240K, Y Chr 46K, and MitoTrio. Each myBaits kit reaction is sufficient to enrich 1 sample.
352016
$3,500
myBaits Expert Human Affinities Kit – Ancestral Plus
Kit for capturing SNPs from human ancient DNA samples. "Ancestral Plus" target set includes 3 premixed probeset modules: Ancestral 850K, Y Chr 46K, and MitoTrio. Each myBaits kit reaction is sufficient to enrich 1 sample.
353016
$3,180
This myBaits Expert kit is available in-stock for quick shipping.


Overview

Development

A team of leaders in ancient human population genetics from multiple institutions contributed to the site selection and protocol development of the myBaits Expert Human Affinities Kit, including:

  • David Reich, Swapan Mallick, and Nadin Rohland of Harvard Medical School [David Reich Lab]
  • Pontus Skoglund of the Francis Crick Institute [Skoglund Lab]
  • Yassine Souilmi, Bastien Llamas, Matthew Williams, and Xavier Roca Rada of the Australian Centre for Ancient DNA [ACAD]

 

Probe Set Composition

The myBaits Expert Human Affinities kit is available in three pre-pooled panel configurations, outlined below. Target files are available on the Resources tab.

myBaits Expert Human Affinities Kits Probe Modules Included
Prime 1240K Ancestral 850K Y Chr 46K MitoTrio
Complete
Prime Plus
Ancestral Plus

Probe Modules

  • Prime 1240K – This target set includes approximately 1.24M SNP sites first described in 2015 (Mathieson et al., Nature) and used in numerous studies since. It contains sites polymorphic in diverse modern and ancient populations. The set includes over 1.15M autosomal sites, 49 K on the X chromosome and 33K on the Y. Module included in Complete and Prime Plus kits.
  • Ancestral 850K – A collection of more than 850K autosomal and X chromosome transversion SNPs ascertained in present-day populations using archaic human genomes as outgroups. This collection reduces bias in population genetic inferences, and mitigates systematic over-differentiation of African from non-African groups common in several datasets. For a detailed explanation of target selection, please review this summary. Module included in Complete and Ancestral Plus kits.
  • Y Chromosome 46K – More than 46K additional Y chromosomal sites identified by the International Society of Genetic Genealogy (ISOGG) that can improve the resolution of patrilineal affiliation within and among groups. Module included in all kits (Complete, Prime Plus, Ancestral Plus).
  • MitoTrio – Probes tiled across three distinct mitochondrial genome references, including the Revised Cambridge Reference Sequence (rCRS), the Reconstructed Sapiens Reference Sequence (RSRS), and that of a Vindija Neanderthal (Genbank NC_011137; Green et al. 2008, Cell). Module included in all kits (Complete, Prime Plus, Ancestral Plus).

 

Population Affinity Inference Capabilities

Sites consistently retrieved in ancient DNA NGS libraries using the myBaits Expert Human Affinities Prime Plus panel provide similar population structure information as the 1240K sites targeted with alternative technology. Population definitions are available here.

Performance

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 30M 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 1.6M 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 30M 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).

Resources

Protocol

Current Version: v1.0

This manual is ONLY compatible with myBaits Expert Human Affinities kits (Cat#’s beginning with 351, 352, or 353).
myBaits Expert Human Affinities Manual

Visit the myBaits manual page to download manuals compatible with other myBaits kits (Custom and Expert).

 

Target Files

Compressed (gzip) BED format files correspond to the hg19 human reference genome [hg19.fa.gz].
Prime 1240K Module – Target BED File
Ancestral 850K Module – Target BED File
Ancestral 850K Module – Target Summary
Y Chromosome 46K Module – Target BED File
MitoTrio Module – Target FASTA File

Please see the README for detailed description of target files.

 

Safety Data Sheets

myBaits Expert Human Affinities Kit SDS – US Version – March 2021
myBaits Expert Human Affinities Kit SDS – EU Version – March 2021

FAQs

Frequently Asked Questions

What sample types are compatible with this kit?

The protocol and reagents provided with the myBaits Expert Human Affinities kit were developed for ancient DNA and other library types that are heavily degraded or contaminated with non-human DNA. It is fully compatible with modern and fresh DNA samples as well.
What protocol should I use with this kit?

myBaits Expert Human Affinities Manual
The protocol and reagents provided with the myBaits Expert Human Affinities kit were developed for ancient DNA and other library types that are heavily degraded or contaminated with non-human DNA. It involves two rounds of hybridization capture, with hybridization incubated at high temperature (70°C), with hybrid bead-binding and washes performed at a lower temperature (55°C or room temperature). Each round involves an over-night incubation, and libraries are amplified following both rounds. When enriching non-contaminated/degraded libraries, a single round of enrichment is recommended.
Are these reagents compatible with other myBaits Custom baits?

No. The myBaits Expert Human Affinities kit is a unique chemistry that should not be coupled with other myBaits Custom or myBaits Expert products. Please contact us for technical questions regarding the use of our products.
What NGS library preparation method should I use for my samples?

The myBaits Expert Human Affinities kit is compatible with virtually any NGS library type that can be amplified with universal primers (before and after capture), including commercial and DIY methods.
Can I pool multiple NGS libraries together for enrichment?

The myBais Expert Human Affinities kit protocol is optimized for degraded and ancient DNA samples to support one NGS library per capture reaction (dual-round enrichment). We do not recommend pooling samples without trials.
Does Daicel Arbor Biosciences perform laboratory services?

Yes, Daicel Arbor Biosciences has an NGS services division adept at preparing and working with ancient DNA libraries. Learn more about our myReads NGS laboratory and sequencing service options, and contact us today to discuss your NGS project goals with our team of ancient DNA experts.

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