deCODE experience Unnur Styrkarsdottir, PhD deCODE Genetics/Amgen, - - PowerPoint PPT Presentation

deCODE genetics

Rare and common variants in complex genetics: the deCODE experience

Unnur Styrkarsdottir, PhD deCODE Genetics/Amgen, Reykjavik, Iceland Rotterdam, November 16th, 2017

• 1. deCODE genetics (Íslensk erfðagreining)

1996 – Owned by Amgen

• 2. An example - rare variant and an indel

associated with osteoarthritis

20 years of genotyping

• Microsatellite panel 1998
• Single Nucleotide polymorphism array 2005
• Whole genome sequencing 2010
• RNA sequencing 2013
• Methylome, Metabolomics, Lipidomics ...

The Icelandic genetics project at deCODE

• Iceland = 340,000 inhabitants
• A founder population
• Genealogy of Icelanders „Book of Icelanders“

– Church + Census (750,000 Individuals)

• Biological samples from 160,000 Icelanders
• Large body of phenotypic information
• Phasing of the genomes and assignment of

parent of origin

Human Phenotype Data

• Over 400 diseases, including sub-phenotypes - close to full spectrum of common

medical conditions

• Hospital records (discharge diagnosis, medical records, pathology)
• Registries (e.g. cancer from 1955, death registry, RAI, drug database)
• Questionnaire based
• Over 600 Quantitative traits
• Anthropometry (Height, Weight, BMI, Body metrics)
• Clinical biological traits routinely measured in blood and urine e.g. lipids
• Computerized electrocardiogram (ECG) and Holter data, echocardiogram
• DXA, MRI, Cognition

• 160,000 chip typed
• 50,000 WGS at ~30X (28,075 in current association

freeze)

• Sequence variations identified by WGS are imputed

into the chip typed Icelanders (and their relatives without genotype information = familial imputation), assisted by long-range phasing

• mRNA sequence data from blood (n=4,000), adipose

(n=1,000) and atrial tissue (n=200)

Human sequence variation data

Father Mother Children

Dataset on diversity in the sequence Dataset on diversity in the phenotype Information for a whole nation Phenotype- Genotype correlation

>1500 phenotypes Whole-genome Sequence (20-30x)

deCODE’s analysis pipeline deCODE Lab

Sample BAM files Sequencing Chip genotyping Chip genotypes BAM genotyping BAM genotypes Sequence genotyping Long range phasing LRP genotypes Sequence genotypes Imputation Imputed genotypes Phenotype lists Phenotype processing Association Marker annotation Annotated Sequence markers Samples Phenotypes Genealogy Association results Functional mutations Sample annotation Sequencing files Alignment Manual processing (data freeze) Automatic processing

deCODE GWAS : Complex Traits association with Common Variants

Type 2 diabetes Myocardial infarction/CAD Abdominal aortic aneurysm Intracranial aneurysm Atrial fibrillation Dementia Stroke Nicotine addiction Lung cancer Peripheral arterial disease Prostate cancer Breast cancer Exfoliation Glaucoma Restless leg syndrome Osteoporosis/BMD Open angle glaucoma Height Pigmentation Melanoma Squamous cell carcinoma Schizophrenia Urinary bladder cancer Asthma Basal cell carcinoma BMI Menarche Thyroid cancer Essential tremor Chronic renal failure Heart block Primary open angle glaucoma Coffee consumption

deCODE GWAS : Complex Traits association with Rare Variants

Ovarian cancer Glioma Basal cell carcinoma of the skin Prostate cancer Cancer of the biliary tract Chronic lymphocytic lymphoma Alzheimer’s Disease Osteoporosis ADHD Type 2 Diabetes Sudden cardiac death Atrial fibrillation Osteoarthritis Gout Age Related Macular Degeneration Dyslexia Schizophrenia Autism Stomach cancer Waldenström’s macroglobulinemia Height Cholesterol and other biological traits Kidney Stones Myocardial Infarctus Hip replacement

Other deCODE data analyses

Recombination rate Gene conversions Mutation rate De novo mutations Parental origin Reproductive sucess Selection Variant landscape in individuals (LoF, missense, etc) Sequences not found in reference genome (non-repetitive)

de novo mutations rate and parents‘ sex and age

Jonsson, et.al. Nature 549, 519–522 (2017)

WGS 1,548 individuals, their parents and for a subset of 225 at least one child 70 de novo mutations per individual, on average The number of de novo mutations increases with age of both fathers (1.5 per year) and mothers (0.37 per year)

• 1. deCODE genetics (Íslensk erfðagreining)

1996 – Owned by Amgen

• 2. An example - rare variant and an indel

associated with osteoarthritis

Rare SNP and recessive Indel - Osteoarthritis

Nature Genetics 49, 801–805 (2017)

WGS Chip array Imputation Association using different models Rare variant Indel RNAseq Public data

GWAS approach

• WGS from 8,453 individuals → 31.6 million variants under the multiplicative model and

19.2 million variants under the recessive model

• Impute into 150,656 chip typed individuals and close relatives (294,212 untyped)
• Select 4,657 Total Hip Replacement cases and 207,514 controls
• Association analysis – multiplicative (additive) and recessive

Rare SNP and recessive Indel - Osteoarthritis

Rare variant only found in Iceland An insertion (8bp) not present

• n chips or other sequencing

datasets (at the time)

A 0.026% variant in COMP - p.asp369his

• Initial imputation information was 0.952 with OR = 10.3 and P = 3.1 × 10-9
• Validate imputation by directly genotyping 82 likely and possible carriers and 253

predicted non-carriers. Add the directly assessed genotypes to the training set for re- imputing.

• Final info 0.996 with OR = 16.7 and P = 4.0 × 10-12
• COMP gene encodes cartilage oligomeric matrix protein = high prior evidence

I II III IV V VI VII

COMP pedigree

Recessive model – very strong signal

8 bp insertion in CHADL gene, p.Val330GlyfsTer106 (frameshift) 3.9% allele freq. / 0.15% recessive Not present in ExAC

Sequencing coverage matters

a b

Black line = total coverage Red line = GC content Black line = Standard True Seq Blue line = True Seq Nano Red line = PCR free

Association driven by rs532464664[insGGCGCGCG]

None of the other variants associated significantly after accounting for the effect of the homozygous state of the rs532464664[insGGCGCGCG] allele (Padj)

Full length CHADL transcript in cartilage

eQTL

CHADL transcript degraded by nonsense mediated decay

Present today in gnomAD browser

We genotyped 10,000 foreign samples in order to estimate frequency in other populations 2% in other European populations compared to 4% in Iceland = founder effect No power to assess recessive association in other populations

Summary COMP - CHADL

• A rare missense SNP in COMP gene associates with THR in Iceland
• Population specific and in one extended pedigree
• Gene with high prior evidence
• Re-genotyping and re-imputation beneficial
• An 8 bp indel in CHADL associates with THR in a recessive manner
• Sequencing coverage crucial
• RNA seq shows expression of full length transcript in cartilage
• Transcript degraded through nonsense mediated decay
• Variants identified through whole genome sequencing used for association analyses
• Population specific imputation based on genealogy and long range haplotypes

Summary deCODE genetics

• Long standing experience of human genetics
• Rich phenotype and genotype data
• Association of common and rare variants with human diseases and traits
• Replications and meta-analyses
• Other basic human genetics analyses

Thank you