README

Daicel Arbor Biosciences
myBaits Expert Human Affinities Kit

Updated March 2021


PROBE MODULE TARGET FILES

Prime 1240K module - https://arborbiosci.com/wp-content/uploads/2021/03/DAB_HumanAffinities-v1_Prime1240K_targets.bed_.gz
Ancestral 850K module - https://arborbiosci.com/wp-content/uploads/2021/03/DAB_HumanAffinities-v1_Ancestral850K_targets.bed_.gz
Y chromosome 46K module - https://arborbiosci.com/wp-content/uploads/2021/03/DAB_HumanAffinities-v1_Ychromo46K_targets.bed_.gz
MitoTrio module (mtDNA) - https://arborbiosci.com/wp-content/uploads/2021/03/DAB_HumanAffinities_Target_MitoTrio.FAS_.txt

BED files refer to the hg19 human reference genome (hg19.fa.gz): http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/

BED file field identifiers (columns):
1) Chromosome on hg19
2) Position of site, 0-based
3) Position of site, 1-based
4) Site name
5) Trial capture membership:
      "Union" = observed in any trial capture
      "Top 3/6/10" = observed in the top 3/6/10 performing captures
      
      
For "Complete" kit targets, combine all 4 target files.
For "Prime Plus" kit targets, combine all target files except for Ancestral 850K.
For "Ancestral Plus" kit targets, combine all target files except for Prime 1240K.


KIT TARGET COMPOSITION

                                   Kits:
Probe Modules:    "Complete"   "Prime Plus"  "Ancestral Plus"
Prime 1240K           X              X
Ancestral 850K        X                             X 
Y chromosome 46K      X              X              X
MitoTrio              X              X              X


PROBE MODULE DEFINITIONS

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.
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.
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.
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).


ADDITIONAL INFO

Technical information about the reagents and protocol for the myBaits Expert Human Affinities Kit can be found in the manual, including troubleshooting tips. Contact techsupport@arbor.daicel.com for additional technical assistance.