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

2. NGS next generation sequencing Camille Flammarion, L‘Atmosphère. Météorologique populaire; Paris 1888

4. as Genetics.

5. Diagnostics at the genetic level: Finding and Characterization 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 rarer forms of diseases. William Harvey (1578–1657) in a letter to the physician Jan Vlackfeld Haarlem, Netherlands, April 24 th, 1657 cf. Groft SC and Posada M (2010) in: Rare Disease Epidemiology, chpt. 1 Adv. Exp. Med. Biol. Vol. 686, pp. 3 –14

7. NGS next generation sequencing WGS whole genome sequencing WES whole exome sequencing PES partial exome sequencing panel

8. WES whole exome sequencing WEA whole exome analysis WGS whole genome sequencing TES targeted exome sequencing WGA whole genome analysis TEA targeted exome analysis all disease genes, ca. 3200 − 4800, e.g. HPO-panel, ca. 2800 genes selected disease genes e.g. Kingsmore-panel, 525 oder 1222 genes NGS: Next Generation Sequencing ca. 20,200 genes, total 50 – 70 Mbp ca. 3.1  10 9 bp

9. THEMED ARTICLE Review The advent of next-generation sequencing technologies has revolutionized the study of genetic variation in the human genome. … and variants detected in noncoding regions remain largely uninterpretable. … … variants detected in noncoding regions remain largely uninterpretable.

10. Pedigree: M 90 00 029 Gene: TLR10 HGNC:15634 OMIM:  606270 Location: 4p14 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 Mutation: Genomic: NC_000004.11:g.38,776,478G>T

11. Database of Genomic Variantion There is no genetic diagnosis (sensu strictu) 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 6. Sequence variation is not known or expected to be causative of disease, but is found to be associated with a clinical presentation

21. Things should be made as simple as possible, but not simpler.

22. Thank You for attention! Feel free to ask questions!

23. MERAP_Introduction_2014apr09