Rapid testing and prenatal diagnosis for at-risk couples presenting during pregnancy without a diagnosis

Transcription

1 Rapid testing and prenatal diagnosis for at-risk couples presenting during pregnancy without a diagnosis Stephen Abbs East Anglian Medical Genetics Service Cambridge University Hospitals NHS Foundation Trust, UK

2 GEMINI GEnomic Medicine INItiative Launched Feb 2014 Prospective diagnostic testing Targeted clinical exome sequencing >1200 clinical samples tested

3 Illumina TruSight One sequencing panel captures and sequences 4813 clinically relevant genes 20,000 GENES 5,000 CLINICALLY RELEVANT

4 Virtual gene panels All 4813 genes sequenced Variants only analysed in clinically relevant genes - avoid incidental findings 226 virtual panels established to date Panels established on demand, 2-3 new panels per week Patients can be tested for multiple panels

5 70 Numbers of genes in all panels No. of panels virtual panels to date Average 11 genes per panel 1195 genes Number of genes in panel

6 Results Mutation(s) No mutation VUS Diagnostic yield Single genes % Panels % Total %

7 Workflow: diagnosis to prenatal testing Diagnostic request Appropriate for clinical exome seqencing? Yes Select/establish virtual gene panel(s) with referring/local consultants Clinical exome sequenced batch of 36 on NextSeq 500 Data filtered Variant analysis in virtual panel(s) Design & order primers, confirm mutations Report No Alternative tests Sequence trio on MiSeq Mutations consistent with disease and inherited Report & offer PND Test parents Prenatal diagnosis

8 Case study 23/12/14 received enquiry about urgent testing for a couple, pregnant, previous child died with suspected Schwartz-Jampel syndrome presenting at birth (radiological and clinical findings) Established appropriate gene panels, with referring Geneticist 6/1/15 DNA received from affected baby and parents Trio sequenced on Illumina MiSeq

9 Schwartz-Jampel syndrome Rare recessive inherited disease abnormalities of skeletal muscle, bone, and cartilage; malformations of the eyes and the face; and growth delays Permanent myotonia (failure of muscles to relax) Skeletal dysplasia, short stature & kyphoscoliosis (curvature of spine) Genes HSPG2 (type 1) and LIFR (type 2) Results filtered for variants in 68 genes (Schwartz-Jampel syndrome; skeletal dysplasia; distal arthrogryposis)

10 HSPG2 homozygous nonsense mutation; diagnosis confirmed gene transcript Position Nucleotide pos Change AA change Score Depth AAF Genotype AF GEMINI Affected HSPG2 NM_ : c C>T p.gln4160 Ter HOMO 0 Mother HSPG2 NM_ : c C>T p.gln4160 Ter HET 0 Father HSPG2 NM_ : c C>T p.gln4160 Ter HET 0

11 HSPG2: c.12478c>t; p.(gln4160ter)

12 Diagnostic referral to prenatal diagnosis 23/12/14 Enquiry 6/1/15 Samples received Trio sequenced on Illumina MiSeq 19/1/15 Results reported (unconfirmed) 27/1/15 Prenatal diagnosis CVS 4 weeks 4 weeks 4/2/15 Prenatal report issued

13 Case study 2 Consanguineous couple referred, pregnant Affected child diagnosed with a Congenital Disorder of Glycosylation (CDG) Trio sequenced and analysed for 19 CDG genes ALG8: c.1135c>t p.(his379tyr) Homozygous affected, heterozygous parents Pregnancy predicted to be unaffected Referral to PND report in 4 weeks

14 Rapid diagnosis and prenatal diagnosis made possible by: A. Flexibility and rapid application of virtual gene panels - allows testing for range of disorders not otherwise available, or requiring multiple tests B. Immediate trio testing - avoids waiting for batch of samples - parental results confirm mutation (recessive and dominant inherited mutations) de novo mutations need confirmation / mosaicism - avoids delays in mutation confirmation process - proceed straight to PND Achievable in 4 weeks Summary

15 Acknowledgements Laboratory: Howard Martin, Fay Rodger, Ruth Littleboy Bioinformatics: Kim Brugger, Matt Garner, Dilna Pushpajan Data analysis & reporting: Isabelle Delon, Olivera Spasic-Boskovic, James Drummond, Ed Thompson, Namir Al-Hasso, Sarah Spiden, Sally Halsall, Harjeet Rai Patient referral: Sarju Mehta, Soo-Mi Park, Ruth Armstrong, Geoff Woods, Simon Holden, Jennifer Campbell, Audrey Smith, Chris Bennett, Richard Sandford, Eamonn Maher et al