DNAVault is built on peer-reviewed science. This page lists the primary references underlying the algorithms, databases, and clinical standards used in the app.
Kinship & Identity by Descent
IBIS: Rapid IBD segment detection Seidman DN, Shenoy SA, Kim M, Babu R, Woods IG, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Williams AL. Rapid, Phase-free Detection of Long Identity-by-Descent Segments Enables Effective Relationship Classification. Am J Hum Genet. 2020;106(4):453–466. PubMed 32197076
KING-robust: Kinship coefficient estimation Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM. Robust relationship inference in genome-wide association studies. Bioinformatics. 2010;26(22):2867–2873. PubMed 20926424
FastIBD: Foundational IBD detection Browning BL, Browning SR. A fast, powerful method for detecting identity by descent. Am J Hum Genet. 2011;88(2):173–182. PubMed 21310274
GERMLINE: Population-scale hidden relatedness Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe’er I. Whole population, genome-wide mapping of hidden relatedness. Genome Res. 2009;19(2):318–326. PubMed 18971310
ERSA: Maximum-likelihood shared ancestry estimation Huff CD, Witherspoon DJ, Simonson TS, et al. Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res. 2011;21(5):768–774. PubMed 21324875
IBD between distant relatives: segment distributions Browning SR, Browning BL. Identity by descent between distant relatives: detection and applications. Annu Rev Genet. 2012;46:617–633. PubMed 22994355
IBD segment length and demographic history Palamara PF, Lencz T, Darvasi A, Pe’er I. Length distributions of identity by descent reveal fine-scale demographic history. Am J Hum Genet. 2012;91(5):809–822. PubMed 23103233
deCODE genetic map: Sex-averaged recombination rates Kong A, Thorleifsson G, Gudbjartsson DF, et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature. 2010;467:1099–1103. PubMed 20981099
Shared cM Project 4.0: Empirical cM ranges by relationship Bettinger BT, Larkin LL, Perl J. The Shared cM Project 4.0 tool v4. DNA Painter. 2020. dnapainter.com/tools/sharedcmv4
Microhaplotype panels for forensic kinship (LR framework) Turchi C, Melchionda F, Pesaresi M, Tagliabracci A. Evaluation of a microhaplotypes panel for forensic genetics using massive parallel sequencing technology. Forensic Sci Int Genet. 2019;41:120–127. PubMed 31071520
Y-DNA Haplogroup Analysis
Yleaf: Y-chromosome haplogroup inference from NGS Ralf A, Montiel González D, Zhong K, Kayser M. Yleaf: Software for Human Y-Chromosomal Haplogroup Inference from Next-Generation Sequencing Data. Mol Biol Evol. 2018;35(5):1291–1294. PubMed 29518227 · PMC6455900
Benchmarking Y haplogroup tools Ralf A, et al. Benchmarking of Y-chromosomal haplogroup determination tools.
Y phylogeny from 1,244 worldwide WGS samples Poznik GD, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 2016;48:593–599. doi:10.1038/ng.3559
yHaplo: Reference-state inclusion for reliable Y calling Poznik GD. Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men. bioRxiv. 2016. GitHub: 23andMe/yhaplo
YFull experimental haplogroup tree (v10.01) 129,000 Y-SNP markers across 39,000 haplogroup nodes. yfull.com/tree
ISOGG Y-DNA haplogroup tree Y-haplogroup naming and lineage reference. isogg.org/tree
Mitochondrial DNA (mtDNA) Haplogroup Analysis
mitoLEAF: mtDNA lineage and evolution framework Huber N, Hurmer N, Dür A, Parson W. mitoLEAF: mitochondrial DNA Lineage, Evolution, Annotation Framework. NAR Genomics Bioinform. 2025;7(2):lqaf079. PubMed 40503051
PhyloTree Build 17: Global mtDNA haplogroup tree van Oven M. PhyloTree Build 17: Growing the human mitochondrial DNA tree.
Cumulative motif definition for mtDNA haplogroups van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat. 2009;30(2):E386–E394. doi:10.1002/humu.20921
rCRS: Cambridge reference sequence for human mtDNA Andrews RM, et al. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 1999;23:147. doi:10.1038/13779
HaploGrep 2: Haplogroup classification with quality scoring Weissensteiner H, et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016;44(W1):W58–W63. doi:10.1093/nar/gkw233
Haplogrep 3: Interactive haplogroup classification platform Schönherr S, et al. Haplogrep 3 — an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 2023;51(W1):W263–W268. doi:10.1093/nar/gkad284
SAM: Polymorphism scoring for forensic mtDNA haplogroup prediction Röck AW, et al. SAM: String-based sequence search algorithm for mitochondrial DNA haplogroup prediction. Int J Legal Med. 2013;127(6):1103–1110.
Health Variants & Clinical Standards
ACMG Secondary Findings v3.2 PubMed 37347242
ACMG Secondary Findings v3.3 PubMed 40568962
ClinVar: NCBI variant clinical significance database NCBI ClinVar. Updated monthly. GRCh38. ncbi.nlm.nih.gov/clinvar
False positive rate of DTC genomic arrays (~40%) PubMed 29565420
Third-party genomic interpretation non-confirmation rate (~75%) PubMed 36327324
ACMG expanded carrier screening recommendations PubMed 34285390
ACMG 2021 technical standard for runs of homozygosity (ROH) PubMed 34906464
Whole Genome Sequencing vs SNP Arrays
WGS adds +5.9% diagnostic yield over SNP arrays PubMed 36907537
WGS diagnostic yield meta-analysis: 38.6% for rare/undiagnosed disease Meta-analysis of 39 studies. OR=1.54 vs WES; standard diagnostics yield 7.8%. PubMed 37231492
Polygenic risk score clinical utility is consistently low PubMed 37133683
Pharmacogenomics
CPIC: 34 genes, 164 drugs for pharmacogenomic interpretation PubMed 37032427 · cpicpgx.org
Cyrius: 99.3% accuracy for CYP2D6 structural allele detection PubMed 33462347
Reference Databases & Tools
Human Phenotype Ontology (HPO) Gene-phenotype mappings with inheritance modes (autosomal recessive, X-linked recessive). hpo.jax.org
gnomAD: Population allele frequency reference gnomad.broadinstitute.org
NCBI RefSeq NC_012920.1 rCRS reference sequence for mtDNA variant calling (16,569 bp). ncbi.nlm.nih.gov/nuccore/NC_012920.1