Are you ready for the genomic age? An introduction to human genomics

Jacques FellayEPFL School of Life SciencesSwiss Institute of BioinformaticsLausanne, Switzerland

What is the genome?

“It's a shop manual, with an incredibly detailed blueprint for building every human cell.It's a history book - a narrative of the journey of our species through time.It's a transformative textbook of medicine, with insights that will give health care providers new powers to treat, prevent and cure disease.”

Francis Collins

Glossary

• Genome: the complete genetic constitution of an organism, encoded in nucleic acids

• Gene: discrete DNA sequence encoding a protein

3 billions base pairs (ATGC)20’000 protein-coding genes

99.6% inter-individual identity (yet 4 millions differences)99% identical to chimpanzee genome (yet 6% different genes)

The human genome

2001: A Species Odyssey

Exploring the human genome

Sanger sequencing,targeted genotyping

Genome-wide genotyping (GWAS)

Exome sequencing

Genome sequencing

2002 2008

International HapMap Project

Identification of common genetic variation in 270 individuals from 4 populations

• CEU: CEPH (Utah residents with ancestry from northern and western Europe) (30 trios)

• CHB: Han Chinese in Beijing, China (45 individuals)• JPT: Japanese in Tokyo, Japan (45 individuals)• YRI: Yoruba in Ibadan, Nigeria (30 trios)

1000 Genomes Project

Whole genome sequencing and complete description of human genetic diversity in >1000 individuals from

multiple world populations

www.1000genomes.org

Short video – Sequencing the genome

http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel

We are all different…

4 million DNA variants / individual

Single nucleotide variants

Multi-nucleotide variants • Small insertions/deletions (indels)• Large copy number variants (CNVs)• Inversions• Translocations • Aneuploidy

Glossary

• SNV = single nucleotide variant: DNA sequence variation in which a single nucleotide — A, T, C or G — differs between members of the same species

• SNP = single nucleotide polymorphism:SNV occurring commonly within a population (> 1%)

SNV/SNP

Glossary

• Allele: One of a number of alternative forms of the same genetic locus (for example a SNP)

About 2% of people have two copies of the APOE4 allele and are very likely to succumb to Alzheimer’s disease

About 1% of us have two copies of a small deletion in CCR5 and are largely immune to infection by the HIV virus

And about 7% do not make any functional CYP2D6 enzyme and therefore codeine provides no pain relief

Glossary

• Linkage Disequilibrium (LD): Non-random association of alleles that descend from single, ancestral chromosomes (i.e. usually close to each other)

• Haplotype: Combination of alleles at adjacent locations on a chromosome that are inherited together

How to read the genome?

Genotyping Sequencing

Glossary

• Genotyping:Process of determining genetic differences between individuals by using a set of markers

• Sequencing:Process of determining the full nucleotide order of a DNA sequence

Genotyping

Genome-wide chips:500K to >1 mio single nucleotide polymorphisms (SNPs)

SNP output

0 2000 4000 6000 8000 10000 12000 14000 16000 18000 20000Intensity (A)

rs1372493

-2000

0

2000

4000

6000

8000

10000

12000

14000

16000

Inte

nsity

(B)

0 0.20 0.40 0.60 0.80 1Norm Theta

rs1372493

-0.20

0

0.20

0.40

0.60

0.80

1

1.20

1.40

1.60

Nor

m R

2317 834 74

Homozygous 1

Heterozygous

Homozygous 2

Genome-wide genotyping

Sequencing

>5%<<<<<1%

Allele frequency of variant

+++ +++

Clinical impact

High-throughput Sequencing (NGS)

– Huge amount of data (terabytes)– Analysis computationally intensive– Dedicated IT infrastructure

• Pipeline

Library construction and sequencing

Sequencing quality controlFASTQ files

FastQ format – single read

@G:1:1:11:1079#0/1

TGATTGATTCCATTCCATTCCATTCCATTTCATTCCATTGCAATCCCTTCCAATCCATTCCATTCCATTCCATTC

+G:1:1:11:1079#0/1`Xa^YO\_^a_`__`a__^a^a^_a``^_\`\\]``[XUGXXXXXWUTWWVWUSTXXPUWYYRVWYYYXZYXYWZ

A complete, high-coverage genome will have over 1 billion reads

• Pipeline

Library construction and sequencing

Sequencing quality controlFASTQ files

Read mappingSort, index, remove duplicates

Mapping quality controlBAM files

• Pipeline

• Pipeline

Library construction and sequencing

Sequencing quality controlFASTQ files

Read mappingSort, index, remove duplicates

Mapping quality controlBAM files

Variant Calling

Variant calling quality controlVCF files

• Pipeline

http://www.ncbi.nlm.nih.gov/core/assets/variation/images/popfreq_example.jpg

Identification of potentially causal variants

Individualized care and counseling

• Pipeline

Library construction and sequencing

Sequencing quality controlFASTQ files

Read mappingSort, index, remove duplicates

Mapping quality controlBAM files

Variant Calling

Variant calling quality controlVCF files

Summary of a single human genome

SNVs 3.5 millionPremature stop 80Stop loss 10Non-synonymousSynonymous

11,00011,000

Essential splice site 25

indels 300,000Frameshift 80In-frame 200

Whole genome vs. exome sequencing

Exome-Coding regions-Cheaper/Faster-Uneven capture of both alleles-Incomplete capture of target region-Bias towards known biology

Genome-Complete sequence

-Expensive/Throughput-IT issues

Clinical sequencing?“Sequencing of the genome or exome for clinical applications has now entered medical practice. Several thousand tests have already been ordered for patients, with the goal of establishing diagnoses for rare, clinically unrecognizable, or puzzling disorders that are suspected to be genetic in origin.”

Leslie G. Biesecker and Robert C. Green, NEJM, 19 June 2014

Clinical sequencing?

TODAY

• Rare functional variants (Mendelian diseases)• Pharmacogenetic variants (150 gene-drug

pairs in the FDA “Table of Pharmacogenomic Biomarkers in Drug Labels”, but only 40 genes involved)

• Oncogenomics

IL28B genotype and response to anti-hepatitis C treatment

Ge, Fellay et al. Nature 2009

Clinical sequencing?

TOMORROW

• Neonatal sequencing• Maternal blood sequencing• DTC genomics brought to doctors

Clinical sequencing?

LATER

• Complex trait genomics (genome data in every health record) – will depend on in-depth understanding of functional genomic variation

Eric Green et al., Charting a course for genomic medicine from base pairs to bedside, Nature 2011

A revolution in the making

Perspective

• Genomic-based medicine is around the corner• Considerable space for new (personal) genomic

market in health, nutrition, well-being…• Genomic-based medicine is only the beginning

of “big-data-based” personalized healthcare

Perspective

None of this can happen without trust