How many personal genomes are available today

1
How many personal genomes are available today?
1. Venter 3X diploid 1.5X haploid 2.
Public HGP haploid 7X 93 1E-4 3. 1000
500K SNPs 3000 Mbp/.5M 1/6000 1 SNPs
33 M 3300 cM What is it? 6E9 bp accuracy
(1E-4 6E5 errors) 1E-9
2
RP11
The human genome project sequence is largely from
one man from Buffalo, NY (code RP11). Out of ten
volunteers in 1997, one male was selected at
random Unfortunately, the attempt to prepare
EBV-transformed cells for the RPCI-11 donor
failed. As a consequence of the double-blind
donor selection procedure, it was impossible to
obtain a second sample from the same male donor
for a second attempt to establish transformed
cells. See (Osoegawa et al 2001). (7X
haploid coverage) Another donor identified
himself in 2002. (3X diploid coverage, no cell
line) Gene DNA (biallelic bp in bold in
central codon) one RP11 allele SLC24A5
A111T atgttgcaggc Rca actttcatggcagcg (Rg
darker skin) OCA2 R305W ccatcagcatc Ygg
gcctccctgcagcag (Yc bluer eyes) OCA2
R419Q accggctctcc cRg ggacgggtgtgggcc (Rg
bluer eyes) Underlined cg dinucleotides
(SLC24A5 15 q21.1 OCA2 15 q11.2-q12 )
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HapMap 270 individuals
Note that the reference RP11 human genome
represents only one of the two alleles (and is a
composite, or missing in 300 regions). Both
alleles are available for HapMap individuals from
Ibadan, Nigeria (YRI), Tokyo, Japan (JPT),
Beijing, China (CHB), Utah, USA (CEU).
Stranger .. Dermitzakis (2007) Science
315848-53. Relative impact of nucleotide and
copy number variation on gene expression
phenotypes. SNPs, CNVs captured 84, 18 of the
total detected genetic variation in 14,925 RNAs
respectively. The International HapMap
Consortium. A haplotype map of the human genome.
Nature 437, 1299-1320. 2005.
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HapMap Success ARMD 50 of variance
ARMD 1q32 Complement Factor H rs1061147
1277T-C exon 9 Li .. Abecasis (2006) CFH
haplotypes without the Y402H coding variant show
strong association with susceptibility to
age-related macular degeneration.Nat Genet. 2006
Sep38(9)1049-54. Maller .. Seddon. (2006)
Common variation in three genes, including a
noncoding variant in CFH, strongly influences
risk of age-related macular degeneration. Nat
Genet.381055-9.
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HapMap Navigation
http//www.hapmap.org/downloads/phasing/2006-07_ph
aseII/00README.txt http//www.hapmap.org/downloads
/phasing/2006-07_phaseII/phased/ genotypes_chr21_C
EU_r21_nr_fwd_legend.txt.gz
20-Jul-2006 1335 256K genotypes_chr21_CEU_r21_
nr_fwd_phased.gz 20-Jul-2006 1335
754K genotypes_chr21_CEU_r21_nr_fwd_sample.txt.
gz 20-Jul-2006 1334 304 legend.txt
rs ID position 0 1 rs11089130
14431347 C G rs915674 14433624 A G
sample.txt ordered list of individual ids that
corresponds to the _phased file. For the CEU and
YRI panels the individual id's are arranged as
follows but the _phased files do not contain the
haplotypes of the children as these can be
inferred from the parents phased one
haplotype per row. For CEU and YRI row 1 -
trio 1 parent 1 transmitted haplotype row 2 -
trio 1 parent 1 untransmitted haplotype row 3 -
trio 1 parent 2 transmitted haplotype row 4 -
trio 1 parent 2 untransmitted haplotype row 5 -
trio 2 parent 1 transmitted haplotype
NA06993 1NA06985 2NA07022 1NA07056 2
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PGP Identity traits, low stigma diseases
(treatable)
Hair Baldness alopecia(minoxidil) Eyes
Near/Far-sightedness(glasses) Iris color
ARMD (glasses) Face Developmental
syndromes, Wrinkles (Botox) Brain
ADHD(Ritalin) Depression(Prozac)
Headache(analgesics) Sleep Circadian
(caffeine, amphetamine, modafinil) Motion
sickness (Dramamine, and Scopolamine) Lip
Cleft palate (surgery) Hirsutism (calcium
thioglycolate) Ears Sensitivity (hearing
aids) Nose Shape breathing disorders
(CPAP) Mouth Halitosis, throat exams aerosols
airborne pathogens Digestion reflux,
gas,ulcer (antibiotics, antacids, PPIs) Skin
Perspiration, Body odor, Pheromones
(deodorants) Surface texture psoriasis
(topicals, photo-treatments) Immune components
acne (topical antibiotics) Skin color vitamin
D sunburn (supplements, SPF cream) Hands
Dermatoglyphics syndromes, Arthritis(corticost
eroids) Internal sensors Proprioceptor,
Repetitive stress (NSAIAs) Body Height Marfan
short stature (hGH) Weight anorexia obesity
(Orlistat, Phentermine, Sibutramine) Allergies
(antihistamines, cortisone, epinephrine,
theophylline) Metabolic polymorphisms (vitamins,
minerals, insulin) Back Strain sensitivity
IDD (analgesics) Feet Plantar fasciitis
(orthotic shoes) Athletes foot (miconazole,
itraconazole, terbinafine, salicylate)
Jon Will DC Down Syndrome 21q22.3
dermatoglyphs
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Self reported Environmental Phenotype data
Nurses health Study (NHS) Personal and
Physical Reproductive History Family
History Environmental, Personal Exposure
Diet and Supplement Use Physical Activity
Screening History Disease Outcomes
Medication Use Psychosocial