Introduction to NGS- based Clinical Diagnosis

1. From NGS Data to Clinical Diagnosis: A Hands-on Wokshop Berlin, April 9th – 10th, 2014 Introduction to NGS-based Clinical Diagnosis Thomas F. Wienker (wienker@molgen.mpg.de) Max-Planck-Institute forMolecularGenetics, Berlin-Dahlem

2. NGS nextgenerationsequencing Camille Flammarion, L‘Atmosphère. Météorologique populaire; Paris 1888

4. asGenetics.

5. Diagnostics atthegeneticlevel: FindingandCharacterization of DNA-Sequencevariants

6. ...there is no better way to advance the proper practice of medicine than to give our minds to the discovery of the usual laws of nature by careful investigation of cases of rarerformsof diseases. cf. Groft SC and Posada M (2010) in: Rare DiseaseEpidemiology, chpt. 1 Adv. Exp. Med. Biol. Vol. 686, pp. 3 –14 William Harvey (1578–1657) in a lettertothephysician Jan Vlackfeld Haarlem, Netherlands, April 24th, 1657

7. NGS nextgenerationsequencing WGS wholegenomesequencing WES wholeexomesequencing PES partial exomesequencing panel

8. NGS: Next Generation Sequencing WGS wholegenomesequencing WGA wholegenomeanalysis ca. 3.1 109bp WEA wholeexomeanalysis WES wholeexomesequencing ca. 20,200 genes, total 50 – 70 Mbp TEA targetedexomeanalysis TES targetedexomesequencing all disease genes, ca. 3200 − 4800, e.g. HPO-panel, ca. 2800 genes selecteddisease genes e.g. Kingsmore-panel, 525 oder 1222 genes

9. THEMED ARTICLE Review The adventofnext-generationsequencingtechnologieshasrevolutionizedthestudyofgeneticvariation in the human genome. …and variantsdetected in noncodingregionsremainlargelyuninterpretable. … … variantsdetected in noncodingregions remainlargelyuninterpretable.

10. Pedigree: M 90 00 029 Gene: TLR10 HGNC:15634 OMIM: 606270 Location: 4p14 Mutation: Genomic: NC_000004.11:g.38,776,478G>T Transcript(s): NM_001017388.2:c.734C>A NM_001195106.1:c.734C>A NM_001195107.1:c.734C>A NM_001195108.1:c.692C>A NM_030956.3:c.734C>A NM_001017388.1:c.734C>A NM_030956.2:c.734C>A Protein: NP_001017388.1(TLR10):p.S245X T/T G/T T/T

11. Database ofGenomicVariantion There is no genetic diagnosis (sensustrictu) outside the framework of the Mendelian paradigm cf. Ken Weiss, TMF−School extra, Berlin, 24. bis 28. September 2012

13. Genome Reference Consortium: GRCh37.p13  hg19 Genome Reference Consortium: GRCh38 [24.12.2013]

15. ECR = expressd cluster regions

16. AGILENT

18. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007 • Genetics IN Medicine, April 2008 Vol. 10 No. 4, 294 -300 • 1. Sequence variation is previously reported and is a recognized cause of the disorder • 2. Sequence variation is previously unreported and is of the type which is expected to cause • the disorder • 3. Sequence variation is previously unreported and is of the type which may or may not • be causative of the disorder • 4. Sequence variation is previously unreported and is probably not causative of disease • 5. Sequence variation is previously reported and is a recognized neutral variant • Sequence variation is not known or expected to be causative of disease, but is found to • be associated with a clinical presentation

21. Things shouldbemade as simple aspossible, but not simpler.

22. ThankYouforattention! Feelfreetoaskquestions!

23. MERAP_Introduction_2014apr09