Supplementary appendix

Transcription

1 Supplementary appendix This appendix formed part of the original submission and has been peer reviewed. We post it as supplied by the authors. Supplement to: Ellingford JM, Sergouniotis PI, Lennon R, et al. Pinpointing clinical diagnosis through whole exome sequencing to direct patient care: a case of Senior-Loken syndrome. Lancet 2015; 35: 1916.

2 (a) (b) (c) proband proband s younger sister Clinical high-throughput DNA sequencing Normal renal function future Ophthalmic diagnosis Ophthalmic diagnosis Molecular diagnosis & renal disease End stage renal failure Figure S1. (a) family pedigree, showing the segregation of IQCB1 c.1119_1120delca (-, deletion present; CA, deletion absent) with infantile-onset retinal dystrophy (closed circles) in a British family. (b) colour fundus photographs, showing the back of the right eye of our case (12 years old; left) and an unaffected control individual (2 years old; right). Attenuation of retinal vessels (arrowheads) and midperipheral fine pigment mottling (asterisk) is observed and is consistent with a rod-cone retinal dystrophy. (c) disease history timeline, showing the order of key clinical events in the proband and his sister.

3 Table S1. Specified transcripts for 105 genes analysed in the proband s DNA after referral to the clinical molecular diagnostic service for inherited retinal disease. HGNC RefSeq Transcript ID HGNC RefSeq Transcript ID HGNC RefSeq Transcript ID ABCA4 NM_ PRPF31 NM_ IMPG2 NM_ ADAM9 NM_ PRPF6 NM_ KCNV2 NM_ AIPL1 NM_ PRPF NM_ KLHL NM_ ARL6 NM_ PRPH2 NM_ IMPG2 NM_ BBS1 NM_ RAX2 NM_ KCNV2 NM_ BBS10 NM_ RBP3 NM_ KLHL NM_ BBS12 NM_ RD3 NM_ LCA5 NM_ BBS2 NM_ RDH12 NM_ LRAT NM_ BBS4 NM_ RDH5 NM_ LRP5 NM_ BBS5 NM_ RGR NM_ MERTK NM_ BBS NM_ RGS9 NM_ MKKS NM_014.2 BBS NM_ RGS9 NM_ MKS1 NM_ BBS9 NM_ RHO NM_ MKS1 NM_01.3 BEST1 NM_ RIMS1 NM_ MYOA NM_ C1QTNF5 NM_ RIMS1 NM_ NDP NM_ C2orf1 NM_ CRB1 NM_ RIMS1 NM_ CA4 NM_ CRX NM_ RLBP1 NM_ CACNA2D4 NM_ DFNB31 NM_ ROM1 NM_ CDH23 NM_ DHDDS NM_024.2 RP1 NM_ CDHR1 NM_ EFEMP1 NM_ RP1L1** NM_15.5 CDHR1 NM_ ELOVL4 NM_ RP2 NM_ CEP290* NM_ EYS NM_ RP9 NM_ CERKL NM_ FAM161A NM_ RPE65 NM_ CHM NM_ FSCN2 NM_ RPGR*** NM_ CLRN1 NM_ FZD4 NM_ RPGRIP1 NM_ CLRN1 NM_ GNAT2 NM_ RS1 NM_ CNGA1 NM_ GPR9 NM_ SAG NM_ CNGA3 NM_ GUCA1A NM_ SEMA4A NM_ CNGB1 NM_ GUCA1B NM_ SNRNP200 NM_ CNGB3 NM_ GUCY2D NM_ SPATA NM_ NR2E3 NM_ IDH3B NM_ TEAD1 NM_ NRL NM_ IDH3B NM_ TIMP3 NM_ OTX2 NM_ IMPDH1 NM_ TOPORS NM_ PCDH15 NM_ IMPG2 NM_ TRIM32 NM_ PCDH15 NM_ KCNV2 NM_ TTC NM_ PCDH15 NM_ KLHL NM_ TULP1 NM_ PCDH15 NM_ LCA5 NM_ UNC119 NM_ PDE6A NM_ LRAT NM_ UNC119 NM_ PDE6B NM_ LRP5 NM_ USH1C NM_ PDE6C NM_ MERTK NM_ USH1C NM_ PDE6G NM_ MKKS NM_014.2 USH1G NM_134.2 PITPNM3 NM_ MKS1 NM_ USH2A NM_ PRCD NM_ MKS1 NM_01.3 ZNF513 NM_ PROM1 NM_ MYOA NM_ PRPF3 NM_ NDP NM_ * Testing of the intronic mutation c a>g in the CEP290 gene is included in this analysis ** Analysis of the coding region of exon 4 of the RP1L1 gene is not included *** Analysis of the coding region of the final exon (orf15) of the RPGR gene is not included

4 Table S2. Selected previously reported cases with the homozygous two nucleotide deletion in IQCB1 (chr3: _ delca, hg19) detected in the proband s DNA sample during the analysis of whole exome sequencing data. Origin Current Parent Affected Age of RD Age of ESRD Reference age consanguinity siblings British 13 No Yes 2 months kidney dysfunction detected before ESRD expected within 6 months This study USA - Not reported Not reported Present, age 15 yrs Brazil - Not reported Not reported Present, age 12 yrs Germany - Not reported Not reported Present, age >10 yrs USA - Not reported Not reported Present, age yrs Germany - No Yes <2 months 12 yrs Germany - No Not reported <2 months <24 yrs Germany - No Not reported Not reported 10 yrs Germany - No Not reported <6 months 15 yrs USA - Not reported Not reported <6 months No manifest renal disease at yrs Abbreviations: RD, retinal disease; ESRD, end stage renal disease. 9

5 Table S3. Predicted consequence of the IQCB1 mutation found in the proband s DNA sample in all transcripts for the IQCB1 gene included in the National Centre for Biotechnology Information Reference Sequence database (NCBI RefSeq). For each transcript the bases deleted from the reference genetic sequence (top) in the proband s DNA sample (bottom) is indicated by red underlined text. The alteration between black and blue text indicates a change in coding exons. Numerical values refer to the relative position of amino acids (single letter amino acid codes included within solid circles: X, stop codon) within the primary structure of the IQCB1 protein. RefSeq ID coding region co-ordinates (hg19) coding region size number of coding region exons Variant annotation NM_ chr3:121,49, ,54,0 5, c.151_1519delca p.his506glnfs*13 Exonic location of variant Expected premature termination 12 in exon 12 NM_ chr3:121,49, ,0 5, c.1119_1120delca p.his33glnfs*13 9 in exon

6 SUPPLEMENTAL REFERENCES 1 McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011; 43: Sherry ST, Ward MH, Kholodov M, et al. dbsnp: the NCBI database of genetic variation. Nucleic Acids Res 2001; 29: Exome Variant Server, NHLBI GO Exome Sequencing Project, Seattle, WA, USA. (Accessed 01/10/2013). 5 Gillespie RL, O'Sullivan J, Ashworth J, et al. Personalized diagnosis and management of congenital cataract by next-generation sequencing. Ophthalmology 2014; 121: The 100,000 Genomes Project, Genomics England, London, UK. (Accessed 14/01/2015). Halbritter J, Porath JD, Diaz KA, et al. Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy. Hum Genet 2013; 132: Otto EA, Loeys B, Khanna H, et al. Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin. Nat Genet 2005; 3: Stone EM, Cideciyan AV, Aleman TS, et al. Variations in NPHP5 in patients with nonsyndromic leber congenital amaurosis and Senior-Loken syndrome. Arch Ophthalmol 2011; 129: 1-.