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The Origin of Ashkenazi Levites
- 1. Doron M Behar, MD, PhD Family Tree DNA, Houston, Texas Estonian Biocentre and Department of Evolutionary Biology University of Tartu, Tartu, Estonia The 11th Genetic Genealogy Conference for Family Tree DNA Group Administrators November 14-15, 2015
- 5. NRY Phylogeny 1997 NRY Phylogeny 2011 5
- 6. Distribution of Hg R1a1-M17/M198 among Ashkenazi Levites 6
- 7. Origin of Ashkenazi Levites A strong founding event within the last 2,000 years >50% of contemporary Ashkenazi Levite Close relatedness to non-Jewish groups Unresolved origin 7
- 8. Global distribution of Hg R1a1 > 2,000 R1a1 samples No good internal structure STR haplotypes are not informative Marker M458 reaches frequencies of 30-70% in East Europe 8
- 9. NGS and its claims April 2009, Complete Genomics: “plan to be able to sequence one million full genomes per year by 2013” June 2009, Illumina: “during the next five years, perhaps markedly sooner, the price point for full genome sequencing will fall from $48,000 to under $1,000”. August 2009, Pacific Biosciences: “will sequence 10,000 full genomes by the end of 2010”. August 2009, GE Global Research: “is also now in the race to commercialize full genome sequencing as they are currently working on creating a service that will deliver a full genome for $1,000 or less”. September 2009, Halcyon Molecular: “will be able to provide full genome sequencing in under 10 minutes for less than $100 per genome”. October 2009, IBM: “they were also in the heated race to provide full genome sequencing for under $1,000, with their ultimate goal being able to provide their service for $100 per genome”.
- 10. Even more claims… March 2010, Pacific Biosciences said: “their second-generation machine, which is scheduled for release in 2015, will be capable of providing a full genome sequence for a person in just 15 minutes for less than $100.” June 2010, Illumina: lowered the cost of its individual sequencing service to $19,500 from $48,000. January 2012, Life Technologies: introduced a sequencer to decode a human genome in one day for $1,000. January 2012, Oxford Nanopore : come up with a DNA sequencing machine (the MinION) the size of a USB memory stick which costs $900 and can sequence simple genomes (but not full human genomes).
- 11. Sequencing Conventional Next generation Sanger based technology A 30 years old monopoly 600-1000 bp per read Reaction time - few hours 10,000,000 reactions to sequence the genome Developed in 2005 by 454 Life Sciences A throughput equivalent to 50 Applied Biosystem's 3730XL capillary sequencers at about one- sixth of the cost
- 12. Data analysis: The NGS bottleneck The flood of information: Data Data Data Changes in data type Accuracy The reference data Not all is in the code
- 13. Pipeline for Whole Y analysis DNA sample Library Preparation Whole Y Capturing Whole Y Sequencing
- 14. The enrichment process A strategy meant to selectively sequence the genomics regions of interest Higher coverage Costly
- 15. Pipeline for Whole Y analysis DNA sample Library Preparation Whole Y Capturing Whole Y Sequencing Raw Data (~100M Reads in FASTQ format) Raw Data Statistics Report Reads Quality Filtering, Trimming Mapping to the Reference Genome (hg19) Mapping Statistics Report
- 18. Quality Control per Whole Y Pre mapping: Total Reads Average Read Length %GC pre-map Post mapping Mapped Reads Average Target Coverage Number of known SNPs
- 19. REF AG ALT A Genotype HOM depth 60 qual_base_calling 214 max qual_mapping 60 max qual_genotype 99 max Quality control per variant
- 20. Pipeline for Whole Y analysis DNA sample Library Preparation Whole Y Capturing Whole Y Sequencing Raw Data (~100M Reads in FASTQ format) Raw Data Statistics Report Reads Quality Filtering, Trimming Mapping to the Reference Genome (hg19) Mapping Statistics Report Variant Calling Annotation of Variants Variants Statistics Report Variants Tables
- 21. How does it look like? Sanger-type sequencing mtDNA mutation m.7572T>C tRNA-Asp region Coverage 2x
- 25. Pipeline for Whole Y analysis DNA sample Library Preparation Whole Y Capturing Whole Y Sequencing Raw Data (~100M Reads in FASTQ format) Raw Data Statistics Report Reads Quality Filtering, Trimming Mapping to the Reference Genome (hg19) Mapping Statistics Report Variant Calling Annotation of Variants Variants Statistics Report Variants Tables Clinical Analysis - Pathogenic Variants Search Final Report File
- 26. Filtering Known phylogeny Y-chromosome regions of intrest Family members Geography
- 27. Example analysis
- 28. Whole Y phylogeny (2015) 28
- 29. Applying to the Levite case 29
- 30. 30
- 32. Meir, Jeff and the Horowitzs 32
- 34. Study design A total of Ashkenazi Levites with carefully revised genealogy (66 samples) Possibly Yeshaya Horowitz descendants (4 samples) A methodological screening of FTDNA database for non-Ashkenazi R1a Obtaining of informed consent (10 samples) Big Y and 111 STRs for all samples 34
- 40. 40
- 42. Tartu Estonian Biocentre Lauri Saag Monika Karmin Mari Järve Siiri Rootsi Mait Metspalu Ene Metspalu Richard Villems Acknowledgements Genealogical peers Meir Garboz Gover Jeff Wexler …& all R1as! Family Tree DNA Connie Bormans Luisa Fernanda Sanchez Brent Manning Uffaf Kahn Annie Gorbet Mark Scheel Claudia Sturman Melissa Grove Elliott Greenspan Bennett Greenspan