Motivations to study human genetic variation The evolution of our species and its history. Understand the genetics of diseases, esp. the more common complex ones such as diabetes, cancer, cardiovascular, and neurodegenerative. To allow pharmaceutical treatments to be tailored to individuals (adverse reactions based on genetics). 1

Haplotype Map of the Human Genome Goals: Define patterns of genetic variation across human genome Guide selection of SNPs efficiently to “tag” common variants Public release of all data (assays, genotypes) Phase I: 1.3 M markers in 269 people Phase II: +2.8 M markers in 270 people

HapMap Project The HapMap Project tests linkage between SNPs in various sub-populations. For a group of linked SNPs recombination may be rare over tens of thousands of bases A few "tag SNPs" can be used to identify genotypes for groups of linked SNPs Makes it possible to survey the whole genome with fewer markers (1/3-1/10th)

Haplotype Linkage is common in the human population, particularly in genetically isolated sub-populations. A group of alleles for neighboring genes on a segment of a chromosome are very often inherited together. Such a combination of linked alleles is known as a haplotype. When linked alleles are shared by members of a population, it is called a linkage disequilibrium.

Haplotypes (example) .. A C T G A chromosome region with only the SNPs shown. Three haplotypes are shown. The two SNPs in color are sufficient to identify (tag) each of the three haplotyes. For example, if a chromosome has alleles A and T at these two tag SNPs, then it has the first haplotype.

HapMap Samples 90 Yoruba individuals (30 parent-parent-offspring trios) from Ibadan, Nigeria (YRI) 90 individuals (30 trios) of European descent from Utah (CEU) 45 Han Chinese individuals from Beijing (CHB) 45 Japanese individuals from Tokyo (JPT)

Make Genetic Profiles Scan these populations with a large number of SNP markers. Find markers linked to drug response phenotypes. It is interesting, but not necessary, to identify the exact genes involved. Can work with “associated populations,” does not require detailed information on disease in family history(pedigree).

The 1000 Genomes Project submitted 17.3M SNPs The SNP database today March, 2010 105,098,087 The 1000 Genomes Project submitted 17.3M SNPs The 2008 SNP Submissions for the James Watson Genome totaled 3,542,364 The 2008 SNP Submissions for the J. Craig Venter Genome totaled 4,018,050 The 2008 SNP Submissions for the Individual Chinese Genome totaled 5,077,954 The 2008 SNP Submissions for the Individual Korean Genome totaled 1,750,224 Derived from dbSNP release 130 http://www.ncbi.nlm.nih.gov/SNP/

SNP’s aren’t everything: Introducing Copy Number Variations Redon et al. Nature 2006

Copy Number Variation Dataset Genome Structural Variation Consortium Array-CGH using a whole genome tile path array Median clone size ~170 kb All 270 HapMap individuals Measures amount of DNA, not RNA Comparison between two samples ‘Test’ sample vs ‘Reference’ sample 10

Array-CGH technology

Typical Analysis Procedure Values are typically normalized so that the mean log2 value for the entire array (or an individual chromosome) is 0 Analysis consists of identifying segments where the test and reference samples have unequal copy number 12

Log(2) = (test/reference) 13

1,447 CNVRs from 270 HapMap samples

More than 10% of the genome sequence Structural Variation Project More than 10% of the genome sequence Nature 447: 161-165, 2007 15

Copy Number Variations are ubiquitous in the human genome The number of genome structural variants (>1 kb) that distinguish genomes of different individuals is at least on the order of 600–900 per individual. J.O. Korbel et al., Science 318(2007), pp. 420–426

HapMap 3 Merged the results from Affymetrix and Illumina chips Genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations Sequenced ten 100-kilobase regions in 692 of these individuals

Centre d’Etude du Polymorphisme Humain collected in Utah, USA, with ancestry from northern and western Europe (CEU) Han Chinese in Beijing, China (CHB) Japanese in Tokyo, Japan (JPT) Yoruba in Ibadan, Nigeria (YRI) African ancestry in the southwestern USA (ASW) Chinese in metropolitan Denver, Colorado, USA (CHD) Gujarati Indians in Houston, Texas, USA (GIH) Luhya in Webuye, Kenya (LWK) Maasai in Kinyawa, Kenya (MKK) Mexican ancestry in Los Angeles, California, USA (MXL) Tuscans in Italy (Toscani in Italia, TSI) CEU, ASW, MXL, MKK, and YRI

Computational detection of structural genomic variation Direct comparison of genomes through sequence alignments Advantages: All types of genomic variation can be identified, including balanced variants (inversions or translocations) No limit in the resolution and breakpoints can be defined at nucleotide level Problems: Generate a lot of false positives due to sequence misassembly and gaps

Out of Africa Modern humans arose in Africa and replaced other human species across the globe. Scientific American, August 1999)

Out of Africa again and again Itai Yanai, 2003 Templeton, A. Nature 416 (2002): 45 - 51

The Human Genome Project cost ~USD 3,000,000,000 Illumina now offers a complete genome sequence from USD 50,000 Complete Genomics will offer a complete genome sequence from USD 5,000 soon There are now an estimated 50 complete human genome sequences

•Craig Venter, Sanger, -$1 million •James Watson, 454. $70 million •Craig Venter, Sanger, -$1 million •African -HapMap –Illumina & Solid, $100,000 •Five African –Penn State University •Chinese, Illumina •Two Koreans •Prof. Quake -Stanford --Nature genetics paper -$50,000, 1 week, Helicos Stanford team -Clinical annotation of genome from “patient Zero”

The 10-gen data set