HumanHap550

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• HumanHap550

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120 samples 28 trios 8 replicates
HumanHap550 Data Quality
Samples by Population
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HumanHap550 Quality Control and Performance
Statistics from FastTrack Genotyping Project Data
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Content Strategy for HumanHap550
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HumanHap550HapMap Coverage by PopulationPairwise
Tests
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HumanHap550 HapMap Coverage by Bin SizePairwise
Tests, r2 0.7, MAF 0.05 CEU Population
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HumanHap550 HapMap Coverage by Bin SizePairwise
Tests, r2 0.7, MAF 0.05CHBJPT Population
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HumanHap550 HapMap Coverage by Bin SizePairwise
Tests, r2 0.7, MAF 0.05YRI Population
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HumanHap550 Coverage of RefSeq Transcripts and
Exons
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HumanHap550 SNP Locations RefSeq Genes
Coverage of transcripts/exons is higher when SNPs
outside exons/transcripts tagging SNPs inside
exons/transcripts are taken into account
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HumanHap550 Spacing by PopulationMAF 0.05
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HumanHap550 Minor Allele Frequency Distribution
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SNPs in Known Copy Number Polymorphic Genomic
Regions

• 4,317 SNPs from 495 regions included in
  HumanHap550
• Regions were identified in 3 recent publications
• Conrad, et al. (Nature Genetics 3875-81, 2006)
• Hinds, et al. (Nature Genetics 3882-85, 2006)
• McCarroll, et al. (Nature Genetics 3886-92,
  2006)
• Proof these regions are actual CNV
• 20X higher Mendelian inconsistency rate compared
  to the rest of HumanHap550 SNPs
• Variations in log R ratios (intensity) in genomic
  profiles

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HumanHap550 Analysis of a Copy Number Polymorphic
Region Using log R Ratios
120 HapMap samples
Published polymorphic region
HumanHap550
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Mitochondrial SNPs

• Mitochondrial genome contains genes involved in
  metabolism and have been implicated in disease
  (i.e., Parkinsons Disease)
• HumanHap550 is the only whole-genome genotyping
  product that contains mitochondrial SNPs
• Selection criteria MAF 0.01 in European
  population, obtained from Broad Institute
  (http//www.broad.mit.edu/mpg/tagger/mito.html)
• 177 mt SNPs on HumanHap550
• Subset of 177 mtSNPs were observed to be
  polymorphic in each population
• 46 SNPs in 33 unrelated CEU individuals
• 48 SNPs in 29 unrelated CHB/JPT individuals
• 60 SNPs in 26 unrelated YRI individuals
• 21 major haplogroups defined in the mitochondrial
  genome by Hernstadt et al (2002)
• 15 / 21 (71) of the major haplogroups are
  represented by haplogroup specific polymorphisms
  on HumanHap550

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HumanHap550 Overlap with Other Standard Products
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HumanHap550 Genotype Files Available Upon Request
Through Tech Support

• Genotype files
• Text file in matrix format
• One file per population
• Alleles called with respect to dbSNP forward
  strand
• File names (size)
• HH550_52dna_Final_Matrix_Report_CEU.txt (91 Mb)
• HH550_30dna_Final_Matrix_Report_CHBJPT.txt (55
  Mb)
• HH550_38dna_Final_Matrix_Report_YRI.txt (68 Mb)
• HH550_120dna_Final_Matrix_Report_ALL.txt (176 Mb)
• Full call reports
• CSV file including genotype, GenCall score and
  normalized X and Y values for each genotype
• One file per population
• Alleles called with respect to dbSNP forward
  strand
• File names (size)
• HH550_52dna_Final_GC_XY_Report_CEU.txt (1.2 Gb)
• HH550_30dna_Final_GC_XY_Report_CHBJPT.txt (688
  Mb)
• HH550_38dna_Final_GC_XY_Report_YRI.txt (871 Mb)
• HH550_118dna_Final_GC_XY_Report_ALL.txt (2.8 Gb)

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HumanHap550 Annotation Files Available Upon
Request Through Tech Support

• HumanHap550_maplocs_and_freqs.tsv (24Mb)
  contains SNP, map information, MAF for each of
  the 3 HapMap populations
• HumanHap550_SNPs_perfect_proxies_ltPOPgt.tsv (where
  ltPOPgt is each of the 3 HapMap populations
  2-7Mb) A list of SNPs in the HumanHap550 panel
  that are in perfect linkage disequlibrium with
  each other. Files for CEU, CHBJPT, and YRI are
  available.
• HumanHap550_v1.0.0_r2_0.7_with_HapMapPhaseIII_ltPO
  Pgt.tsv (where ltPOPgt is each of the 3 HapMap
  populations 50-127Mb) This file contains
  linkage disequilibrium annotation of the
  HumanHap550 SNPs with respect to HapMap Phase I
  II SNPs. All pairwise correlations between a
  HumanHap550 SNP and common HapMap SNPs (MAF gt
  0.05) with r2 gt 0.7 are listed. The region
  spanned by the HapMap SNPs and the genes found in
  that region /-10 kb are listed.
• HumanHap550_v1.0.0_GeneAnnotation.txt (42Mb)
  contains SNP, map information, gene annotation
• HumanHap550_v1.0.0_SNP_nsSNP_annotation.csv
  (1Mb) Contains gene and nsSNP annotation for the
  7,779 nonsynonymous SNPs in the HumanHap550