Southern California Genealogical Society Jamboree
Genetic Genealogy 2022
Online Virtual Conference
LIVE: FRIDAY & SATURDAY
AUGUST 19-20, 2022
- World-class DNA Conference
- Get in on the Latest Discoveries
- Learn from over 20 renowned Genetic Genealogy experts
- All purchased Genealogy Jamboree presentations viewable through October 31, 2022.
See conference Web Site for registration and viewing information
Overview
Going from dozens of STR markers to millions of SNP results in the Big Y (and similar) DNA tests is a huge jump in complexity. Session will address advanced topics such as: (1) how the terminal SNP and phylogenetic tree are determined; (2) BAM file use in comparing novel variants between matching individuals; (3) incorporating sampling context into genealogical and geographic interpretations.
Here is a list of references, resources, and additional information relating to the presentation for Intermediate and Advanced Y-DNA Topics at SCGS Jamboree 2022:
Web References
- Margaryan et al (2020), Population genomes of the Viking world, Nature Vol 585 doi:10.1038/s41586-020-2688-8
- YFull.com (2022) Haplogroup YTree v10.03.00 (16 May 2022) https://www.yfull.com/tree
- Wikipedia, “List of countries by population (United Nations)”
https://en.wikipedia.org/w/index.php?oldid=879939654 - Wikipedia, “Countries of the United Kingdom by population”
https://en.wikipedia.org/w/index.php?oldid=869454643 - Wikipedia, “World Map of Y-DNA Haplogroups”
Image by Chakazul 2013 https://commons.wikimedia.org/w/index.php?title=File:World_Map_of_Y-DNA_Haplogroups.png&oldid=333927556 - Wikipedia, “FASTA format”
https://en.wikipedia.org/w/index.php?title=FASTA_format&oldid=1076840315 - Wikipedia, “Variant Call Format”
https://en.wikipedia.org/wiki/Variant_Call_Format - Illumina, “FASTQ files explained”
https://support.illumina.com/bulletins/2016/04/fastq-files-explained.html - Rugare Maruzani (2021), “How to Download NGS Data From NCBI’s Sequence Read Archive”
https://towardsdatascience.com/how-to-download-ngs-data-from-ncbis-sequence-read-archive-ead03908a192 - Li, et al (2009), “The Sequence Alignment/Map format and SAMtools”, Bioinformatics (Oxford, England), 25(16), 2078–2079. doi:10.1093/bioinformatics/btp352
- Michael F Hammer et al as the Y Chromosome Consortium in “A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups” in Genome Research journal 12:339-348 by Cold Spring Harbor Laboratory Press, www.genome.org.
https://genome.cshlp.org/content/12/2/339.full - Gross (2007), “A New Human Genome Sequence Paves the Way for Individualized Genomics Gross”, L PLoS Biology Vol. 5, No. 10, e266. doi:10.1371/journal.pbio.0050266
- Wikipedia, Human Genome Project
https://en.wikipedia.org/wiki/Human_Genome_Project - Telomere-to-Telomere (T2T) Consortium
https://sites.google.com/ucsc.edu/t2tworkinggroup - University of California, Santa Cruz (UCSC), “Sequence and Annotation Downloads”
https://hgdownload.soe.ucsc.edu/downloads.html#human - Nurk et al (2022), “The complete sequence of a human genome”. Science 2022 Apr;376(6588):44-53,
doi:10.1126/science.abj6987 - Zimin et al (2021) A reference-quality, fully annotated genome from a Puerto Rican individual, doi:10.1101/2021.06.10.447952
- YDNA-Warehouse, Telomere-to-Telomere Y Chromosome Experiments,
https://ydna-warehouse.org/t2t-experiments - Genome Reference Consortium
https://www.ncbi.nlm.nih.gov/grc - Genome Research Limited, SAMtools Download
https://www.htslib.org/download/ - GitHub repository for samtools for Windows x64 by Doug Xie (xied75)
https://github.com/xied75/samtools - Darby et al (2016), Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing. doi:10.1002/ece3.2221
- YouTube video, “Introduction to Burrows-Wheeler Alignment and SAMtools for Cancer Mutation Calling Bioinformatics 1″
https://www.youtube.com/watch?v=P_YKQKFI4Lk - Family Tree DNA (2019), Big Y Results Matching in FTDNA Learning Center. Retrieved 11:00, January 30, 2019.
https://www.familytreedna.com/learn/y-dna-testing/big-y/big-y/ - Family Tree DNA, [Big Y-700] Big Y Whitepaper by Davis, Sager, et al. (22 Mar 2019)
https://blog.familytreedna.com/wp-content/uploads/2019/03/big-y-700-white-paper_compressed.pdf - Family Tree DNA, [Original] Big Y Whitepaper (August 2014)
https://www.familytreedna.com/learn/wp-content/uploads/2014/08/BIG_Y_WhitePager.pdf - Family Tree DNA (2019), Y-DNA Haplotree public tool.
https://www.familytreedna.com/public/y-dna-haplotree - Thomas Krahn’s YSeq Laboratory for STR, SNP, and WGS testing
https://www.yseq.net - Full Genomes Corp for lowest cost sequencing (performed in China)
https://www.fullgenomes.com - YFull DNA Interpretation Services (Russia)
https://www.yfull.com - Michael F Hammer et al as the Y Chromosome Consortium in “A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups” in Genome Research journal 12:339-348 by Cold Spring Harbor Laboratory Press, www.genome.org.
doi:10.1101/gr.217602 - B. Charlesworth (2003), The organization and evolution of the human Y chromosome, in Genome Biology, 4:226, BioMed Central Ltd.
doi:10.1186/gb-2003-4-9-226 - Khan Academy, Building a phylogenetic tree (2015).
https://www.khanacademy.org/science/biology/her/tree-of-life/a/building-an-evolutionary-tree - Genealogy of Jesus of Nazareth, The Bible, Book of Mathew, Chapter 1, published by The International Bible Society.
https://www.biblica.com/bible/niv/matthew/1/ - GeneticHomeland.com (2022), DNA Marker Index
https://www.genetichomeland.com/welcome/dnamarkerindex.asp - GeneticHomeland.com (2022), DNA Ancestral Pedigree Tree.
https://www.genetichomeland.com/welcome/dnapedigree.asp - Skaletsky et al (2003), The male-specific region of the Y chromosome is a mosaic of discreet sequence classes, Nature, Vol 423,
doi:10.1038/nature01722 - Family Tree DNA, Why Family Tree DNA?, About The Family Tree DNA Database,
https://www.familytreedna.com/why-ftdna.aspx -
Irish Mapping DNA Project at Family Tree DNA, Project Statistics,
https://www.familytreedna.com/groups/irishmapping/about/project-statistics - International Society of Genetic Genealogy, Wiki, Y-DNA SNP testing chart
https://isogg.org/wiki/Y-DNA_SNP_testing_chart - ISOGG Y-DNA Haplotree with SNP naming prefixes
https://isogg.org/tree - Nebula Genomics
https://nebula.org/whole-genome-sequencing-dna-test - GenoHub (2022), “Choosing the Right NGS Sequencing Instrument for Your Study”
https://genohub.com/ngs-instrument-guide - National Human Genome Research Institute (NHGRI)
Diagram of double helix DNA structure by artist Darryl Leja
http://www.genome.gov/12514471 - NCBI Sequence Read Archive (SRA), “Download” page
https://www.ncbi.nlm.nih.gov/home/download
https://www.ncbi.nlm.nih.gov/sra - NCBI GenBank database search, “Nucleotide – NCBI”
https://www.ncbi.nlm.nih.gov/nuccore?db=nucleotide - ENA – European Nucleotide Archive
https://www.ebi.ac.uk - 1000 Genomes Project (1KGP)
https://www.internationalgenome.org - Human Genome Diversity Project (HGDP)
https://www.internationalgenome.org/data-portal/data-collection/hgdp - Simons Genome Diversity Project (SGDP)
https://www.simonsfoundation.org/simons-genome-diversity-project
data available at Seven Bridges Cancer Genomics Cloud
https://cgc-accounts.sbgenomics.com - Estonian Biocentre
https://evolbio.ut.ee - IGV BAM File Viewer
http://software.broadinstitute.org/software/igv/download
- ISOGG YBrowse, Human Y Chromosome Pangenome Browser
https://ybrowse.org/gb2/gbrowse/chrY - Nature Education (2008), “Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups”
https://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956 - Tiger Walsh (2019), “Giant Tree of Mankind’s Paternal Lineages” image on “R1b All Subclades” DNA Project at FTDNA
https://www.familytreedna.com/groups/r-1b/about/background - Costa (2017), “Genetics – Haplogroups” message board
https://www.theapricity.com/forum/showthread.php?213740-Most-common-Y-DNA-haplogroup-by-country - Brad Larkin (2014), “Ancestral Parish Sampling for Genetic Genealogy”, Surname DNA Journal
https://www.surnamedna.com/wp-content/uploads/2014/02/AncestralParishSampling.pdf - Brad Larkin (2013), “Y-DNA of the British Monarchy”, Surname DNA Journal
doi:10.14487/sdna.000675