Clinical Genomics – infrastructure for

translational research at Karolinska Institutet

& Science for Life Laboratory

Several strong genomics infrastructures are available at SciLifeLab

Clinical Genomics – Translational research bringing NGS based technologies to diagnostic use

NGI – To make NGS techniques available for researchers in Sweden, to enable internationally competitive research and to provide scientific support.

Functional Genomics – To provide infrastructure for example for screening assays and various single-cell based assays

WABI / BILS– Project-based bioinformatics support

State-of-the-art NGS support available for both basic and translational research

Mission statement• To make a state-of-the-art infrastructure for

massively parallel DNA sequencing and SNP genotyping available to researchers in Sweden.

• To enable Swedish scientists to perform internationally competitive research in genomics.

• To provide guidelines and support for sample collections, study design and protocol selection.

Vision• To contribute to best possible patient care

Mission statement• To create a state-of-the-art infrastructure for

translational research enabling clinical diagnostic analyses of patient samples

• To introduce and validate the utility in routine medical care

• To carry out the work in a manner that is competitive on an international level

Basic research Translational research

StatisticsIn 2014 27,000 samplesIn 2015 (est) >30,000 samples

StatisticsIn 2014 1,000 samplesIn 2015 (est) >2,000 samples

Clinical / medical sequencing expected to drive the future growth of the next-generation sequencing market

Clinical Genomics to supports transition of NGS from research to health care use.

Basic research

[NGI, WABI and others]

Translational research

[Clinical Genomics]

Routine diagnostics

[Health care sector]

Translational research (Phase 2)•Proof-of-principle demonstrations

Translational research (Phase 3)•Demonstration of utility•Long-term projects, 2-5 years

Clinical Genomics has a complete infrastructure established for clinical-grade NGS operations

Translational NGS

ISO 17025 accreditation

Sequencing capacity

Library prepa-rations

Personnel

Bioinfor-matics

Premises

Compu-tational capacity

Storage capacity

Agilent Bravo liquid handlersCovaris S2, Covaris 96KingFisher, qPCR, Fragment Analyzer, etc

4 Lab6 IT/Bioinformatics2 Management

Close collaboration with clinical collaboratorsAutomated pipelines

Custom-built premises, 300 sqmEnhanced security enabling analysis of patient samples

Dedicated secure systems384 CPU; 12,000 core hours / month

Redundant data storage for all on-going analyses. Backup on tape

11 HiSeq 2500 (Illumina)3 MiSeq (Illumina)

5 HiSeq X (Illumina)

Microbial applications

Exome sequencing based applications

Establishing a close collaboration with Karolinska university hospital

• Centrum för medfödda metabola sjukdomar• Anna Wedell• Inborn errors of metabolism

• Klinisk immunologi/transfusionsmedicin• Charlotta Wikström• Primary immunodeficiencies

• Klinisk Genetik• Magnus Nordenskjöld• Skeletal dysplasia• Neuromuscular disorders• Syndromes

• 2015: Non-invasive prenatal diagnostics (NIPT)

• Klinisk mikrobiologi• Tobias Allander• Microbial identification using 16S• Outbreak analysis• The ‘unknown’ sample

• Covering population of approx 2.5 M• 1.5 M patient visits in 2013• 1600 beds• Turnover 15.7 BSEK / 2.2 BUSD (2013) • National responsibility for certain disease areas

New Karolinska hospital under construction

Example - Clinical Genomics’ sample-to-results pipeline for rare monogenic disorders

Delivery to SciLifeLab Manual or Automated library preparations

Rapid sequencing on HiSeq 2500

Dedicated HPC cluster for data processing

Alignment, variant call, functional annotation(Henrik Stranneheim, CMMS, KS)GeneMod (Måns Magnusson, KI)

Sample specific quality measurement (Chanjo)

Browser-based data presentation for collaborating physicians

Automated, secure data processing and QC

The EHEC Outbreak May - June 2011

• 53 Swedish cases in total• 18 (34 %) of these were HUS cases• 1 of the HUS cases died• 1 domestic case was an outlier• 48 isolates were typed to the outbreak strain

Tunisia 2010 is the most similarstrain isolated prior to the outbreak

Sweden 2011Germany 2011France 2011

Tunisia 2010

100%

Germany 2001

Central Africa 2000

39 SNPs

322 SNPs

2465 SNPs

1-7 SNPs

The VRE outbreaksUppsala, 2014 & 2015

PFGE – Gold standard for VRE typing

NGS

• Cultivation of VRE on blood agar plates and enrichment in BHI

• DNA extraction with MagNaPure Compact

• SciLifeLab, Clinical Genomics

• 70 strains sequenced (= 70 x ~3 Mb , 30 x coverage)

vanA

vanA 50G

Results all outbreaks

vanB 30EvanB 70C

vanB unik

vanB Tierp

vanB 30C

vanA

vanA 50G

Results all outbreaks

vanB 30EvanB 70C

vanB unik

vanB Tierp

vanB 30CEfmB 1308

EfmA 1410

EfmB 1509

EfmB 1402

Activities Clinical Genomics facility (Stockholm)Rare inherited monogenic disorders

Discovery Test pilot Validation Real-timevalidation

Stranneheim et al,BMC Genomics, 2014

Clinical exome sequencing

Clinical test/accreditation Publications

Clinical WGS (repl exome)

Clinical acute setting WGS

NIPT

Structural variants (WGS, mate-pair)

Hofmeister et al, J Med Gen, 2014

Prenatal diagnostics

PGD

CRC (rand, d-b, clin trial)Cancer

Panel

BC (prospective study) Panel, low-pass WGS, RNA seq

Pancreatic (PCM) Exome (300x/150x)

Neuroblastoma WGS (70x/35x)

AML Panel, l-p WGS, RNA, RNA fus

Personlised immunotherapy Exome (300x/150x)

16SMicrobiology

Outbreak (WGS)

Surveillance (WGS)

’The unknown’ sample Metagenomics

Microbiome 16S, Metagenomics Engstrand-Lilja et al, Microbiome, 2015

Sequencing capacity 2006 vs 2015 - great impact on high-throughput WGS

Per instrument: 1800 Gb / run600 Gb / day3 days / human genomePer 10 instruments:18,000 human genomes per year

0.5 Gb / run0.5 Gb / day240 days / human genome

WGS 10 000 Swedish bacterial strains – national project

• Use of HiSeq X plaform (2000 strains/run)

• Optimize lib prep (dilution of Nextera kit)

• DNA extraction at home lab• 30 x coverage• Defined metadata• Bioinformatic support

• Outbreaks• Surveillance (Sweden/EU)• CCUG• Ab resistance collections• More…..