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ONLINE APPENDIXMETHODS1. Whole genome sequencing, data processing, and variant calling1.1. Genome sequencingWhole genome sequencing was performed at the Kinghorn Centre for Clinical Genomics facility, New South Wales, Australia, or at the Macrogen facility, Seoul, Republic of Korea. TruSeq Nano libraries (Illumina, San Diego, CA) were prepared according to the manufacturer's recommendations and 2 x 150 bp paired-end sequencing was performed on a HiSeq X Ten sequencer (Illumina). 1.2. Sequence read alignment and post-alignment processingSequencing reads were aligned to the human genome reference (hs37d5) using bwa-mem (v0.7.10), converted to binary with Samtools (v0.1.19), and duplicate reads removed using Novosort (v1.03.01). Intervals for sequence read realignment were determined using the Genome Analysis Tool Kit v3.3.0 (GATK) RealignerTargetCreator, and local realignment was performed using GATK IndelRealigner. Base quality scores were recalibrated using GATK BaseRecalibrator with a list of known polymorphic single nucleotide variants and short insertions and deletions. New base quality scores were applied using GATK PrintReads.1.3. Sequence read depth calculationPicard tools (v2.1.1) was used to collect read depth metrics for each sample. Read depth metrics of each sample were calculated from binary alignment map files using Illumina’s coverage calculation method: ((MEAN_COVERAGE ) × ( 1 - PCT_EXC_DUPE - PCT_EXC_OVERLAP ))/ ( 1 - PCT_EXC_TOTAL )1.4. Variant calling and annotationGATK HaplotypeCaller module was used to generate a genome variant call file (gvcf) for each sample, and joint genotyping was then performed on all gvcf files using GATK GenotypeGVCFs module. Variants were filtered using GATK VariantRecalibrator with a set of known polymorphic single nucleotide variants and short insertions and deletions. Variants sites passing quality filters were normalized using bcftools to separate multi-allelic sites, and annotated using ENSEMBL Variant Effect Predictor (VEP). To annotate variants, the RefSeq gene and transcript annotations were used (--refseq) and we excluded predicted transcripts (--exclude_predicted). Protein coding RefSeq transcripts used to annotate variants within the 184 target genes were manually selected based on the principal (longest protein coding) isoform, or known essential cardiac transcript isoforms, and are shown in online table 2.2. Gene collation2.1. Online Mendelian Inheritance in Man databaseGenes that could cause cardiac hypertrophy were retrieved from the Online Mendelian Inheritance in Man (OMIM) database, Accessed 15th May 2017, using the following search terms:'cardiomyopathy, hypertrophic', 'cardiomyopathy, familial hypertrophic', 'danon disease', 'fabry disease', 'glycogen storage disease', 'noonan\|costello\|cardiofaciocutaneous', 'cardiomyopathy, dilated', 'dilated cardiomyopathy', 'leigh syndrome', 'mitochondrial complex deficiency', and 'mitochondrial DNA deletion syndrome'.2.2. NCBI Genetic Testing Registries A list of gene targets for genetic testing of hypertrophic cardiomyopathy were retrieved from the Genetic Testing Registry, accessed 15 May, 2017. ()2.3. Recent literature searchA search of recent literature for genes associated with cardiac hypertrophy or hypertrophic cardiomyopathy was performed using PubMed. We retrieved one novel gene (ALPK3), associated with autosomal recessive, childhood onset, hypertrophic cardiomyopathy (PMID: 26846950).3. Large genomic rearrangement analysis3.1 LUMPY analysisLarge deletions, inversions and translocations were found using LUMPY, which integrates information from discordant read pairs and split reads. Discordantly mapped paired end reads and split reads were extracted using Samtools (v0.1.19). The mean distance of 100,000 mapped reads was determined using the provided Python script (pairend_distro.py). Deletions, inversions and translocations were extracted using LUMPY from discordant and split read alignment regions with a read depth <150 reads, which overlapped with at least one protein coding exon of 184 genes that cause cardiac hypertrophy.3.2 CNVnator analysisCopy number variants were found using CNVnator (v0.3.3), which uses read depth analysis of genome sequencing data. The genome is divided into equal segments and the read depth signal for each segment is calculated, and corrected for bias introduced by GC content.4. Validation of potential novel splice sites.4.1 RNA extractionRNA was extracted using Trizol (Thermo Fisher Scientific, Massachusetts, USA). 10 mls fresh venous blood was mixed with 40 mls blood lysis buffer (320 mM sucrose, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1% Triton-X-100) and stored on ice for 20 minutes. Following centrifugation at 1400 rpm for 10 minutes, the peripheral blood lymphocyte cell pellet was resuspended in 1 ml Trizol and RNA was extracted according to manufacturer’s recommendations.4.2 Reverse transcription PCR1 ug RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen), at 55C for 1 hour, according to manufacturer’s recommendations, except with 10pM of a gene specific primer. 2.5ul of complementary cDNA was amplified with polymerase chain reaction using the same reverse primer as used in the reverse transcription step, plus a second gene specific forward primer annealing at least two exons upstream. PCR was performed using GoTaq polymerase (Promega Inc.) at 60C annealing temperature for 35 cycles. Amplification products were resolved using agarose gel electrophoresis. MYH7 AGCCTTTTAGAGCCGGGGGGATTCCAGTGGAGGGGTCCAGGCGGTGGGTCTGAGCCCTTTMYH6 AGCTTTTCAGAGCCGGGGGGATTCCAGTGGAGGGGTCCAGGCGGTGGGTCTGAGCCCTTT *** *** ****************************************************MYH7 GTGTCTGACC-AGGCACGCATCGAGGAGCTGGAGGAGGAGCTGGAGGCCGAGCGCACCGCMYH6 GTGTCTGACCCAGGCACGCATCGAGGAGCTGGAGGAGGAGCTGGAGGCCGAGCGCACCGC ********** *************************************************MYH7 CAGGGCTAAGGTGGAGAAGCTGCGCTCAGACCTGTCTCGGGAGCTGGAGGAGATCAGCGAMYH6 CAGGGCTAAGGTGGAGAAGCTGCGCTCAGACCTGTCTCGGGAGCTGGAGGAGATCAGCGA ************************************************************MYH7 GCGGCTGGAAGAGGCCGGCGGGGCCACGTCCGTGCAGATCGAGATGAACAAGAAGCGCGAMYH6 GCGGCTGGAAGAGGCCGGCGGGGCCACGTCCGTGCAGATCGAGATGAACAAGAAGCGCGA ************************************************************MYH7 GGCCGAGTTCCAGAAGATGCGGCGGGACCTGGAGGAGGCCACGCTGCAGCACGAGGCCACMYH6 GGCCGAGTTCCAGAAGATGCGGCGGGACCTGGAGGAGGCCACGCTGCAGCACGAGGCCAC ************************************************************MYH7 TGCCGCGGCCCTGCGCAAGAAGCACGCCGACAGCGTGGCCGAGCTGGGCGAGCAGATCGAMYH6 TGCCGCGGCCCTGCGCAAGAAGCACGCCGACAGCGTGGCCGAGCTGGGCGAGCAGATCGA ************************************************************MYH7 CAACCTGCAGCGGGTGAAGCAGAAGCTGGAGAAGGAGAAGAGCGAGTTCAAGCTGGAGCTMYH6 CAACCTGCAGCGGGTGAAGCAGAAGCTGGAGAAGGAGAAGAGCGAGTTCAAGCTGGAGCT ************************************************************MYH7 GGATGACGTCACCTCCAACATGGAGCAGATCATCAAGGCCAAGGCAGGCTCTGCTCGGCCMYH6 GGATGACGTCACCTCCAACATGGAGCAGATCATCAAGGCCAAGGCAGGCTCTGCTCGGCC ************************************************************MYH7 TCCCCTCCTCMYH6 TCCCCTC--- ******* Online Figure 1. Alignment of 486 bp sequence duplication of MYH7 and MYH6. Sequence alignment of MYH7 (chr14:23889027-23889515) and MYH6 (chr14:23859242-23859729) homologous sequence, with asterisk indicating identical nucleotides. Underlined sequence corresponds to exon 27 of MYH7 and MYH6. Location of MYH7 c.3523C>T variant found in BIJ1 is highlighted red. Online Figure 2. Genome sequencing reveals an MYH7 Arg1175Trp variant. A) Exome sequence reads are shown as white horizontal bars, indicating a mapping quality of zero (upper panel); genome sequence reads are shown as grey horizontal bars, indicating a high mapping quality (lower panel). B) Sanger verification of an MYH7 Arg1175Trp variant in patient BIJ1 and a control. Online Figure 3. Characterization of a 4,080 bp deletion of TK2. A). Exon structure flanking deleted region of TK2, with arrow showing direction of transcription. Genome sequence reads at the deletion locus, with split reads across the deleted region shown in brown. B) Exon structure and Sanger sequencing of the TK2 deletion breakpoint.Online Figure 4. Characterization of a 4,080 bp duplication. A) Duplicated locus showing direction of transcription of ANO8 and GTPBP3 genes, with Sanger sequencing electropherogram of duplication boundaries. B) Orientation of duplicated 7,807 bp segment. Online Table 1. Genome sequencing metricsSample IDMean coverageFraction of genome covered 10XFraction of genome covered 20XFraction of genome covered 30XAB144.670.980.950.87AC145.780.980.950.87ACC142.380.980.940.81ACU137.450.970.950.69ACU245.190.970.970.92AEV144.710.980.940.84AHQ145.490.980.950.89AIB145.090.980.950.88AIB246.310.980.950.89AIH146.140.980.950.89AJ139.640.980.930.74AJ234.330.970.890.51AK141.220.970.960.82AKP143.710.970.970.90AKQ144.210.980.950.87ALG141.260.970.960.83AQT141.690.970.960.85AQT242.110.980.940.82AZS144.520.980.950.87BCT145.040.980.950.87BIJ142.390.980.940.81BKJ140.760.980.930.78BKJ245.700.980.950.88BL146.650.980.950.88BNP241.550.980.930.80BNR143.770.970.960.88BNV144.490.980.950.86BOI143.630.980.940.85BOQ144.580.980.950.87DA145.520.980.950.88DH147.110.980.970.93DJ145.030.980.950.88DJ246.190.980.950.88DK145.730.980.950.88E242.400.980.940.84E338.010.980.920.72EX145.450.980.950.87GB146.600.980.950.89GM131.210.970.880.45GM232.090.970.870.39GM331.730.970.880.52ID140.200.970.960.83ID241.990.970.960.86ID439.940.970.960.81IP142.460.980.940.84JR146.080.980.950.89KM147.200.980.950.89LE143.570.980.940.85LF148.740.980.970.94LU143.490.980.950.85MJ146.480.970.970.92NB145.810.970.970.92NG143.230.980.940.84NU146.100.970.970.92NU443.420.980.950.86OL146.230.980.950.88OM143.740.980.950.86OO145.570.970.970.91OR148.300.980.960.90PM146.760.980.950.89PT146.610.980.950.88QX140.800.980.940.80SU146.430.980.950.89SU245.650.970.970.92SW139.300.970.960.79SW237.610.980.920.71SW338.010.980.920.72T145.100.980.950.87T438.080.980.920.69TC147.020.980.950.89TF148.270.980.960.90VE146.520.980.950.88XC142.430.980.940.83ZH144.000.980.950.86Online Table 2. Coverage metrics for 25 hypertrophic cardiomyopathy associated genesGeneMean coverage of geneMean percentage of exonic bases covered by 15 or more readsACTC141.4100.00ACTN244.999.69CALR344.5100.00CAV343.6100.00CSRP343.3100.00FLNC46.0100.00JPH245.999.07LDB342.799.88MYBPC343.099.99MYH646.7100.00MYH741.3100.00MYL241.1100.00MYL343.7100.00MYLK243.3100.00MYOZ243.5100.00MYPN41.9100.00NEXN43.9100.00PLN43.8100.00TCAP43.6100.00TNNC143.2100.00TNNI348.399.99TNNT239.4100.00TPM141.899.99TTN44.0100.00VCL41.7100.00Online Table 3. 184 candidate cardiac hypertrophy genesGeneRefSeq TranscriptInheritance modeRelevant OMIM phenotypeOMIM search termHypertrophic cardiomyopathy established genes (n=8)MYBPC3NM_000256.3ADCardiomyopathy, hypertrophic, 4, 115197 (3)Cardiomyopathy, hypertrophicMYH7NM_000257.2ADCardiomyopathy, hypertrophic, 1, 192600 (3)Cardiomyopathy, hypertrophicTNNT2NM_001001430.2ADCardiomyopathy, hypertrophic, 2, 115195 (3)Cardiomyopathy, hypertrophicTNNI3NM_000363.4ADCardiomyopathy, hypertrophic, 7, 613690 (3)Cardiomyopathy, hypertrophicTPM1NM_001018005.1ADCardiomyopathy, hypertrophic, 3, 115196 (3)Cardiomyopathy, hypertrophicACTC1NM_005159.4ADCardiomyopathy, hypertrophic, 11, 612098 (3)Cardiomyopathy, hypertrophicMYL2NM_000432.3ADCardiomyopathy, hypertrophic, 10, 608758 (3)Cardiomyopathy, hypertrophicMYL3NM_000258.2ADCardiomyopathy, hypertrophic, 8, 608751 (3)Cardiomyopathy, hypertrophicHypertrophic cardiomyopathy implicated genes (n=17)ACTN2NM_001103.3ADCardiomyopathy, hypertrophic, 23, with or without LVNC, 612158 (3)Cardiomyopathy, hypertrophicCALR3NM_145046.4ADCardiomyopathy, hypertrophic, 19, 613875 (3)Cardiomyopathy, hypertrophicCSRP3NM_003476.4ADCardiomyopathy, hypertrophic, 12, 612124 (3)Cardiomyopathy, hypertrophicJPH2NM_020433.4ADCardiomyopathy, hypertrophic, 17, 613873 (3)Cardiomyopathy, hypertrophicLDB3NM_007078.2ADCardiomyopathy, hypertrophic, 24, 601493 (3)Cardiomyopathy, hypertrophicMYH6NM_002471.3ADCardiomyopathy, hypertrophic, 14, 613251 (3Cardiomyopathy, hypertrophicMYLK2NM_033118.3ADCardiomyopathy, hypertrophic, 1, digenic, 192600 (3)Cardiomyopathy, hypertrophicMYOZ2NM_016599.4ADCardiomyopathy, hypertrophic, 16, 613838 (3)Cardiomyopathy, hypertrophicMYPNNM_032578.3ADCardiomyopathy, hypertrophic, 22, 615248 (3)Cardiomyopathy, hypertrophicNEXNNM_144573.3ADCardiomyopathy, hypertrophic, 20, 613876 (3Cardiomyopathy, hypertrophicPLNNM_002667.3ADCardiomyopathy, hypertrophic, 18, 613874 (3)Cardiomyopathy, hypertrophicTCAPNM_003673.3ADCardiomyopathy, hypertrophic, 25, 607487 (3)Cardiomyopathy, hypertrophicTNNC1NM_003280.2ADCardiomyopathy, hypertrophic, 13, 613243 (3)Cardiomyopathy, hypertrophicVCLNM_014000.2ADCardiomyopathy, hypertrophic, 15, 613255 (3)Cardiomyopathy, hypertrophicCAV3NM_001234.4ADCardiomyopathy, familial hypertrophic, 192600 (3)Cardiomyopathy, familial hypertrophicFLNCNM_001458.4ADCardiomyopathy, familial hypertrophic, 26 (3)Cardiomyopathy, familial hypertrophicTTNNM_003319.4; NM_133378.4ADCardiomyopathy, familial hypertrophic, 9, 613765 (3)Cardiomyopathy, familial hypertrophicPhenocopies of hypertrophic cardiomyopathy (n=2)LAMP2NM_013995.2X-linkedDanon disease, 300257 (3)Danon diseaseGLANM_000169.2X-linkedFabry disease, 301500 (3)Fabry diseaseGlycogen storage disease genes (n=17)AGLNM_000642.2ARGlycogen storage disease IIIa, 232400 (3)Glycogen storage diseaseALDOANM_184043.2ARGlycogen storage disease XII, 611881 (3)Glycogen storage diseaseENO3NM_001976.4ARGlycogen storage disease XIII, 612932 (3)Glycogen storage diseaseG6PCNM_000151.3ARGlycogen storage disease Ia, 232200 (3)Glycogen storage diseaseGAANM_000152.3ARGlycogen storage disease II, 232300 (3)Glycogen storage diseaseGBE1NM_000158.3ARGlycogen storage disease IV, 232500 (3)Glycogen storage diseaseGYG1NM_004130.3ARGlycogen storage disease XV, 613507 (3Glycogen storage diseaseGYS1NM_002103.4ARGlycogen storage disease 0, muscle, 611556 (3)Glycogen storage diseaseGYS2NM_021957.3ARGlycogen storage disease 0, liver, 240600 (3)Glycogen storage diseaseLDHANM_005566.3ARGlycogen storage disease XI, 612933 (3)Glycogen storage diseasePFKMNM_000289.5ARGlycogen storage disease VII, 232800 (3)Glycogen storage diseasePGAM2NM_000290.3ARGlycogen storage disease X, 261670 (3)Glycogen storage diseasePHKA2NM_000292.2X-linkedGlycogen storage disease, type IXa1, 306000 (3)Glycogen storage diseasePHKG2NM_000294.2ARGlycogen storage disease IXc, 613027 (3)Glycogen storage diseasePRKAG2NM_016203.3ADGlycogen storage disease of heart, lethal congenital, 261740 (3)Glycogen storage diseasePYGLNM_002863.4ARGlycogen storage disease VI, 232700 (3)Glycogen storage diseaseSLC37A4NM_001467.5ARGlycogen storage disease Ib, 232220 (3)Glycogen storage diseaseNoonan syndrome/ Costello syndrome/ Cardiofaciocutaneous syndrome genes (n=15)BRAFNM_004333.4ADNoonan syndrome 7, 613706 (3); LEOPARD syndrome 3, 613707 (3NoonanCBLNM_005188.3ADNoonan syndrome-like disorder with or without juvenile myelomonocytic leukemia, 613563 (3)NoonanKRASNM_004985.3ADNoonan syndrome 3, 609942 (3)NoonanLZTR1NM_006767.3ADNoonan syndrome 10, 616564 (3)NoonanNF1NM_000267.3ADNeurofibromatosis-Noonan syndrome, 601321 (3)NoonanNRASNM_002524.4ADNoonan syndrome 6, 613224 (3)NoonanPTPN11NM_002834.3ADNoonan syndrome 1, 163950 (3); LEOPARD syndrome 1, 151100 (3)NoonanRAF1NM_002880.3ADNoonan syndrome 5, 611553 (3)NoonanRIT1NM_006912.5ADNoonan syndrome 8, 615355 (3)NoonanSHOC2NM_007373.3ADNoonan-like syndrome with loose anagen hair, 607721 (3)NoonanSOS1NM_005633.3ADNoonan syndrome 4, 610733 (3)NoonanSOS2NM_006939.2ADNoonan syndrome 9, 616559 (3)NoonanHRASNM_005343.2ADCostello syndrome, 218040 (3)CostelloMAP2K1NM_002755.3ADCardiofaciocutaneous syndrome 3, 615279 (3)CardiofaciocutaneousMAP2K2NM_030662.3ADCardiofaciocutaneous syndrome 4, 615280 (3)CardiofaciocutaneousDilated cardiomyopathy genes (n=20)ABCC9NM_005691.2ADCardiomyopathy, dilated, 1O, 608569 (3)Cardiomyopathy, dilatedBAG3NM_004281.3ADCardiomyopathy, dilated, 1HH, 613881 (3)Cardiomyopathy, dilatedCRYABNM_001885.1ADCardiomyopathy, dilated, 1II, 615184 (3)Cardiomyopathy, dilatedDESNM_001927.3ADCardiomyopathy, dilated, 1I, 604765 (3)Cardiomyopathy, dilatedDMDNM_004006.2X-linkedCardiomyopathy, dilated, 3B, 302045 (3)Cardiomyopathy, dilatedDSG2NM_001943.3ADCardiomyopathy, dilated, 1BB, 612877 (3)Cardiomyopathy, dilatedDSPNM_004415.2ARCardiomyopathy, dilated, with woolly hair and keratoderma, 605676 (3)Cardiomyopathy, dilatedEYA4NM_004100.4ADCardiomyopathy, dilated, 1J, 605362 (3)Cardiomyopathy, dilatedFKTNNM_006731.2ARCardiomyopathy, dilated, 1X, 611615 (3)Cardiomyopathy, dilatedGATAD1NM_021167.4ARCardiomyopathy, dilated, 2B, 614672 (3)Cardiomyopathy, dilatedLAMA4NM_002290.4ADCardiomyopathy, dilated, 1JJ, 615235 (3Cardiomyopathy, dilatedLMNANM_170707.3ADCardiomyopathy, dilated, 1A, 115200 (3)Cardiomyopathy, dilatedPRDM16NM_022114.3ADCardiomyopathy, dilated, 1LL, 615373 (3)Cardiomyopathy, dilatedPSEN1NM_000021.3ADCardiomyopathy, dilated, 1U, 613694 (3)Cardiomyopathy, dilatedPSEN2NM_000447.2ADCardiomyopathy, dilated, 1V, 613697 (3)Cardiomyopathy, dilatedRBM20NM_001134363.1ADCardiomyopathy, dilated, 1DD, 613172 (3)Cardiomyopathy, dilatedSCN5ANM_198056.2ADCardiomyopathy, dilated, 1E, 601154 (3)Cardiomyopathy, dilatedSDHANM_004168.2ADCardiomyopathy, dilated, 1GG, 613642 (3)Cardiomyopathy, dilatedSGCDNM_000337.5ARCardiomyopathy, dilated, 1L, 606685 (3Cardiomyopathy, dilatedTNNI3KNM_015978.2ADCardiac conduction disease with or without dilated cardiomyopathy, 616117 (3)Dilated cardiomyopathyMitochondrial disease genes (n=68)COX15NM_078470.4ARLeigh syndrome due to cytochrome c oxidase deficiency, 256000 (3)Leigh syndromeNDUFA10NM_004544.3ARLeigh syndrome, 256000 (3)Leigh syndromeNDUFA12NM_018838.4ARLeigh syndrome due to mitochondrial complex 1 deficiency, 256000 (3)Leigh syndromeNDUFA2NM_002488.4ARLeigh syndrome due to mitochondrial complex I deficiency, 256000 (3)Leigh syndromeNDUFA9NM_005002.4ARLeigh syndrome due to mitochondrial complex I deficiency, 256000 (3)Leigh syndromeNDUFAF6NM_152416.3ARLeigh syndrome due to mitochondrial complex I deficiency, 256000 (3)Leigh syndromeNDUFS3NM_004551.2ARLeigh syndrome due to mitochondrial complex I deficiency, 256000 (3)Leigh syndromeNDUFS7NM_024407.4ARLeigh syndrome, 256000 (3)Leigh syndromeNDUFS8NM_002496.3ARLeigh syndrome due to mitochondrial complex I deficiency, 256000 (3)Leigh syndromeSURF1NM_003172.3ARLeigh syndrome, due to COX IV deficiency, 256000 (3)Leigh syndromeATP5A1NM_004046.5ARMitochondrial complex (ATP synthase) deficiency, nuclear type 4, 615228 (3)Mitochondrial complex deficiencyNDUFAF5NM_024120.4ARMitochondrial complex 1 deficiency, 252010 (3)Mitochondrial complex deficiencyACAD9NM_014049.4ARMitochondrial complex I deficiency due to ACAD9 deficiency, 611126 (3)Mitochondrial complex deficiencyFOXRED1NM_017547.3ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFA1NM_004541.3X-linkedMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFA11NM_175614.4ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFAF1NM_016013.3ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFAF2NM_174889.4ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFAF3NM_199069.1ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFAF4NM_014165.3ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFB11NM_001135998.2X-linkedMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFB3NM_002491.2ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFB9NM_005005.2ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFS1NM_005006.6ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFS2NM_004550.4ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFS4NM_002495.2ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFS6NM_004553.4ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFV1NM_007103.3ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNDUFV2NM_021074.4ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyNUBPLNM_025152.2ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencyTMEM126BNM_018480.4ARMitochondrial complex I deficiency, 252010 (3)Mitochondrial complex deficiencySDHAF1NM_001042631.2ARMitochondrial complex II deficiency, 252011 (3)Mitochondrial complex deficiencySDHDNM_003002.3ARMitochondrial complex II deficiency, 252011 (3)Mitochondrial complex deficiencyBCS1LNM_004328.4ARMitochondrial complex III deficiency, nuclear type 1, 124000 (3)Mitochondrial complex deficiencyTTC19NM_017775.3ARMitochondrial complex III deficiency, nuclear type 2, 615157 (3)Mitochondrial complex deficiencyUQCRBNM_006294.4ARMitochondrial complex III deficiency, nuclear type 3, 615158 (3)Mitochondrial complex deficiencyUQCRQNM_014402.4ARMitochondrial complex III deficiency, nuclear type 4, 615159 (3)Mitochondrial complex deficiencyUQCRC2NM_003366.2ARMitochondrial complex III deficiency, nuclear type 5, 615160 (3)Mitochondrial complex deficiencyCYC1NM_001916.3ARMitochondrial complex III deficiency, nuclear type 6, 615453 (3)Mitochondrial complex deficiencyUQCC2NM_032340.3ARMitochondrial complex III deficiency, nuclear type 7, 615824 (3)Mitochondrial complex deficiencyLYRM7NM_181705.2ARMitochondrial complex III deficiency, nuclear type 8, 615838 (3)Mitochondrial complex deficiencyUQCC3NM_001085372.2ARMitochondrial complex III deficiency, nuclear type 9, 616111 (3)Mitochondrial complex deficiencyAPOPT1NM_032374.3ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyCOX10NM_001303.3ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyCOX14NM_032901.3ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyCOX20NM_198076.4ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyCOX6B1NM_001863.4ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyCOX8ANM_004074.2ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyFASTKD2NM_014929.3ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyPET100NM_001171155.1ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencySCO1NM_004589.2ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyTACO1NM_016360.3ARMitochondrial complex IV deficiency, 220110 (3)Mitochondrial complex deficiencyATPAF2NM_145691.3ARMitochondrial complex V (ATP synthase) deficiency, nuclear type 1, 604273 (3)Mitochondrial complex deficiencyTMEM70NM_017866.5ARMitochondrial complex V (ATP synthase) deficiency, nuclear type 2, 614052 (3)Mitochondrial complex deficiencyATP5ENM_006886.3ARMitochondrial complex V (ATP synthase) deficiency, nuclear type 3, 614053 (3)Mitochondrial complex deficiencyDGUOKNM_080916.2ARMitochondrial DNA depletion syndrome 3 (hepatocerebral type), 251880 (3)Mitochondrial DNA depletion syndromeFBXL4NM_012160.4ARMitochondrial DNA depletion syndrome 13 (encephalomyopathic type), 615471 (3)Mitochondrial DNA depletion syndromeMGME1NM_052865.2ARMitochondrial DNA depletion syndrome 11, 615084 (3)Mitochondrial DNA depletion syndromeMPV17NM_002437.4ARMitochondrial DNA depletion syndrome 6 (hepatocerebral type), 256810 (3)Mitochondrial DNA depletion syndromeOPA1NM_130836.2ARMitochondrial DNA depletion syndrome 14 (encephalocardiomyopathic type), 616896 (3)Mitochondrial DNA depletion syndromeRRM2BNM_015713.4ARMitochondrial DNA depletion syndrome 8A (encephalomyopathic type with renal tubulopathy), 612075 (3)Mitochondrial DNA depletion syndromeSLC25A4NM_001151.3ADMitochondrial DNA depletion syndrome 12A (cardiomyopathic type), 617184 (3)Mitochondrial DNA depletion syndromeSUCLA2NM_003850.2ARMitochondrial DNA depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria), 612073 (3)Mitochondrial DNA depletion syndromeSUCLG1NM_003849.3ARMitochondrial DNA depletion syndrome 9 (encephalomyopathic type with methylmalonic aciduria), 245400 (3)Mitochondrial DNA depletion syndromeTFAMNM_003201.2ARMitochondrial DNA depletion syndrome 15 (hepatocerebral type), 617156 (3)Mitochondrial DNA depletion syndromeTK2NM_004614.4ARMitochondrial DNA depletion syndrome 2 (myopathic type), 609560 (3)Mitochondrial DNA depletion syndromeTWNKNM_021830.4ARMitochondrial DNA depletion syndrome 7 (hepatocerebral type), 271245 (3)Mitochondrial DNA depletion syndromeTYMPNM_001953.4ARMitochondrial DNA depletion syndrome 1 (MNGIE type), 603041 (3)Mitochondrial DNA depletion syndromeGenetic testing registry additional genes (n=36)AARS2NM_020745.3ARCombined oxidative phosphorylation deficiency 8naACADVLNM_000018.3ARVery long chain acyl-CoA dehydrogenase deficiencynaAGKNM_018238.3ARCataract and cardiomyopathynaAGPAT2NM_006412.3ARCongenital generalized lipodystrophy type 1naAMER1NM_152424.3X-linkedOsteopathia striata with cranial sclerosisnaANKS6NM_173551.3ARNephronophthisis 16naBSCL2NM_032667.6ARCongenital generalized lipodystrophy type 2naCACNA1CNM_000719.6ADTimothy syndromenaCOA5NM_001008215.2ARCardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 3naCOQ2NM_015697.7ARCoenzyme Q10 deficiency, primary 1naCYB5R3NM_000398.6ARDeficiency of cytochrome-b5 reductasenaELAC2NM_018127.6ARCombined oxidative phosphorylation deficiency 17naFAHNM_000137.2ARTyrosinemia type InaFHL1NM_001159699.1X-linkedMyopathy with postural muscle atrophy, X-linkednaFTONM_001080432.2ARGrowth retardation, developmental delay, coarse facies, and early death; naFXNNM_000144.4ARFriedreich ataxia 1naGLB1NM_000404.2ARGangliosidosis GM1 type 3; GM1 gangliosidosis type 2; Infantile GM1 gangliosidosisnaGNPTABNM_024312.4ARI cell disease; Pseudo-Hurler polydystrophynaGTPBP3NM_032620.3ARCombined oxidative phosphorylation deficiency 23naHADHNM_005327.4ARDeficiency of 3-hydroxyacyl-CoA dehydrogenasenaHCCSNM_005333.4X-linkedLinear skin defects with multiple congenital anomalies 1naHSD17B10NM_004493.2X-linked2-methyl-3-hydroxybutyric aciduria; Mental retardation, X-linked, syndromic 10naKLF1NM_006563.3ARCongenital dyserythropoietic anemia, type IVnaLIASNM_006859.3ARPyruvate dehydrogenase lipoic acid synthetase deficiencynaMLYCDNM_012213.2ARDeficiency of malonyl-CoA decarboxylasenaMRPL3NM_007208.3ARCombined oxidative phosphorylation deficiency 9naMRPL44NM_022915.3ARCombined oxidative phosphorylation deficiency 16naMRPS22NM_020191.2ARCombined oxidative phosphorylation deficiency 5naMTO1NM_012123.3ARCombined oxidative phosphorylation deficiency 10naSCO2NM_005138.2ARCardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiencynaSLC22A5NM_003060.3ARRenal carnitine transport defectnaSLC25A3NM_021977.3ARMitochondrial phosphate carrier deficiencynaSMC1ANM_006306.3X-linkedCongenital muscular hypertrophy-cerebral syndromenaTAZNM_181311.2X-linked3-Methylglutaconic aciduria type 2; Primary dilated cardiomyopathynaTMEM126ANM_032273.3AROptic atrophy 7naYARS2NM_001040436.2ARMyopathy, lactic acidosis, and sideroblastic anemia 2; ; naRecently reported genes associated with hypertrophic cardiomyopathy (n=1)ALPK3NM_020778.4ARJ Am Coll Cardiol. 2016 Feb 9;67(5):515-25.naAD - autosomal dominant; AR - autosomal recessive; OMIM - Online Mendelian Inheritance in Man.Online Table 4. Patient clinical details and demographicsPatientCohortSexAge at diagnosis(years)PresentationFamily history of cardiomyopathy or sudden cardiac death(number affected)MaxIVS(mm)MaxLV(mm)Pattern of hypertrophySurgical interventionsSudden cardiac death eventNumber of appropriate ICD dischargesPrevious genetic testing approach(number of genes analyzed)AB11M3SymptomaticNo2525ASHICDmyectomyAppropriate ICD shock2MPS gene panel (46)AC11M33Asymptomatic (incidental)No1616ConcentricICDheart transplantNo0MPS gene panel (65)ACU11F23SymptomaticYes, HCM (5)2525ASHNoNoNAMPS exome (46)ACU21FNot reportedNot reportedYes, HCM (5)---NoNoNANoneAHQ11M41SymptomaticNo2525ASHICD PPMmyectomyOHCA0MPS gene panel (46)AIB11M23SymptomaticYes, HCM (2)1818ASHNoNoNAMPS gene panel (65)AIB21MNot reportedNot reportedYes, HCM (2)1515Not reportedNoNoNANoneAIH11M35SymptomaticNo2929ASHICD PPMNo0MPS gene panel (46)AJ11M14Asymptomatic (family screening)Yes, HCM (4)2727ASHNoNoNAMPS gene panel (64)AJ21M0.5SymptomaticYes, HCM (4)2126ASHMyectomyNoNANoneAK11F25Asymptomatic (incidental)Yes, HCM (2)3333ASHICD myectomyNo0Sanger (7)AKP11F20Asymptomatic (incidental)Yes, HCM (5)2626ASHICDNo0MPS gene panel (46)AKQ11M15Asymptomatic (incidental)No1120ApicalNoNoNAMPS gene panel (46)AQT11F33SymptomaticYes, HCM (2)1722ApicalNoNoNAMPS gene panel (65)AQT21M52Asymptomatic (family screening)Yes, HCM (2)1717ASHNoNoNANoneAZS11M56Asymptomatic (incidental)Yes, HCM (2)1818ApicalNoNoNAMPS gene panel (46)BCT11M45SymptomaticNo2727ASHICDOHCA0MPS gene panel (65)BIJ11M52SymptomaticYes, HCM (2)1919ASHNoNoNAMPS exome (46)BKJ11M12Asymptomatic (incidental)Yes, HCM (3)2222ASHMyectomyNoNAMPS exome (46)BKJ21M14Asymptomatic (incidental)Yes, HCM (3)2020ASHICDNo0NoneBL11M36SymptomaticNo3737ASHICD heart transplantAppropriate ICD shock3MPS gene panel (46)DA11M29SymptomaticNo3838ASHICDAppropriate ICD shock4MPS gene panel (46)DJ11M16SymptomaticYes, HCM (2)2828ASHICD AF ablationNo0MPS exome (46)DJ21M31SymptomaticYes, HCM (2)1515ConcentricAF ablationNoNAMPS exome (46)DK11M33Asymptomatic (incidental)Yes, HCM (3)3030ASHICDNo0MPS exome (46)E21M43Asymptomatic (family screening)Yes, HCM (3)1818ConcentricNoNoNAMPS exome (46)E31M68Asymptomatic (family screening)Yes, HCM (3)2222Not reportedICDOHCA; appropriate ICD shock1MPS exome (46)EX11M45SymptomaticNoNot reportedNot reportedNot reportedICDOHCA; appropriate ICD shock6MPS gene panel (46)GB11M58SymptomaticYes, HCM (4)2323ASHICD myectomyNo0MPS gene panel (46)GM11F5SymptomaticNo4242ASHICD PPMAppropriate ICD shock; SCD4MPS gene panel (46)GM21FNAUnaffectedNo1010Not applicableNoNoNANoneGM31MNAUnaffectedNoNot reportedNot reportedNot applicableNoNoNANoneID11F39SymptomaticYes, HCM (5) + SCD (1)1919ASHNoNoNAMPS exome (46)ID21F29SymptomaticYes, HCM (5) + SCD (1)4343ASHICD PPM myectomy ablationAppropriate ICD shock1MPS gene panel (46)ID41F19SymptomaticYes, HCM (5) + SCD (1)2121ASHNoNoNANoneIP11M30SymptomaticYes, HCM (2)1616ConcentricNoNoNAMPS gene panel (46)JR11M15Asymptomatic (incidental)Yes, HCM (2) + SCD(1)1414ConcentricICDNo0MPS gene panel (46)LE11M44Not reportedYes, HCM (2)2323ASHNoNoNAMPS gene panel (46)LF11F59SymptomaticYes, HCM (5)1616ASHNoNoNAMPS gene panel (46)LU11M53SymptomaticNo1323ApicalICDOHCA0MPS gene panel (46)MJ11F47SymptomaticYes, HCM (2) + SCD(1)1616ASHICDOHCA; appropriate ICD shock1MPS gene panel (46)NB11M14Asymptomatic (incidental)No1717ASHNoNoNAMPS gene panel (46)NG11M48Asymptomatic (incidental)Yes, HCM (2)1423ASHICDNo0MPS gene panel (46)NU11F56SymptomaticYes, HCM (4) + SCD (1)1818ASHICDNo0MPS gene panel (46)NU41M36Asymptomatic (family screening)Yes, HCM (4) + SCD (1)2526ASHNoNoNANoneOM11M11Asymptomatic (family screening)Yes, HCM (2)2929ASHICDNo0Sanger (11)OO11F33Asymptomatic (incidental)Yes, HCM (2)1313ASHICD heart transplantNo0MPS gene panel (46)OR11M18SymptomaticNo2222ASHNoNoNAMPS gene panel (46)PM11M34SymptomaticNo2525ASHICDAppropriate ICD shock2MPS gene panel (46)PT11M31Asymptomatic (incidental)Yes, HCM (2)2323ASHNoNoNASanger (10)QX11M44SymptomaticNo2020ConcentricNoNoNASanger (11)SU11M16Asymptomatic (family screening)Yes, HCM (2)2424ASHNoNoNASanger (10)SU21F52Asymptomatic (incidental)Yes, HCM (2)1616ASHNoNoNANoneSW11F56SymptomaticYes, HCM (4)1616ASHNoNoNAMPS gene panel (46)SW21M31Asymptomatic (family screening)Yes, HCM (4)1919ASHNoNoNAMPS exome (46)SW31M39SymptomaticYes, HCM (4)2323ASHMyectomyNoNAMPS exome (46)T11M45Asymptomatic (family screening)Yes, HCM (2) + SCD (1)1515ASHNoNoNAMPS gene panel (46)T41M14SymptomaticYes, HCM (2) + SCD (1)2020ASHNoSCDNANoneTC11M23SymptomaticYes, HCM (3)3333ASHICD PPMNo0Sanger (11)VE11M9Asymptomatic (incidental)Yes, ARVC (1)2323ASHNoNoNAMPS exome (46)XC11M38SymptomaticNo3535ASHICDNo0MPS gene panel (46)ZH11M42Asymptomatic (incidental)Yes, HCM (2)3333ASHICDNo0MPS gene panel (46)ACC12M80Not reportedYes, SCD (1)1919ConcentricNoNoNANoneAEV12M29Asymptomatic (incidental)No3434ASHICD PPMNo0NoneALG12F16SymptomaticYes, HCM (3)3030ASHICD PPMNo0NoneBNP22M18Asymptomatic (family screening)Yes, HCM (7), SCD (1)2626ASHNoNoNANoneBNR12F56SymptomaticYes, HCM (2)Not reportedNot reportedNot reportedNoNoNANoneBNV12M21Asymptomatic (incidental)No2424ASHNoNoNANoneBOI12MNANot reportedYes, HCM (2) + SCD (1)Not reportedNot reportedNot reportedNoNoNANoneBOQ12M25Asymptomatic (incidental)Yes, HCM (2)1919ASHNoNoNANoneDH12F49SymptomaticYes, HCM (2)2323ASHNoNoNANoneKM12M31SymptomaticYes, HCM (2)1121ApicalICDNo0NoneOL12M56SymptomaticNo1115ASHICD PPMNo0NoneTF12M27Asymptomatic (incidental)Yes, SCD (1)3131ASHICD PPMNo0NoneIVS - interventricular septum; LV - left ventricle; ICD - implantable cardioverter defibrillator; ASH - asymmetric septal hypertrophy; MPS - massively parallel sequencing; PPM - permanent pacemaker; OHCA - out of hospital cardiac arrest; SCD - sudden cardiac death; NA - not applicable Online Table 5. Variants of uncertain clinical significancea) Variants of uncertain clinical significance in autosomal dominant disease genesFamilyPatient CohortGenecDNA changeConsequencegnomAD allele countPolyPhen HumDivSIFTGERPCADDClinvar IDClinvar ClassificationAB11TTNNM_133378.4:c.30859A>GLys10287Glu1possibly damaging-6.0222.5 not reportednaAHQ11LAMA4NM_002290.4:c.105C>GAsp35Glu4probably damagingdeleterious4.4327.2 not reportednaAIH11FLNCNM_001458.4:c.2818A>GMet940Val0benigntolerated5.325.455 not reportednaAIH11TTNNM_133378.4:c.8056A>GIle2686Val2benign-2.449.378 not reportednaAIH11FHL1NM_001159699.1 c.817G>CVal273Leu8benigntolerated-0.7418.636 not reportednaAQT1 AQT21NF1NM_000267.3 c.1987G>AGly663Arg6benigntolerated5.2620.9RCV000415075 RCV000163499 RCV000206471VUSBIJ11MYH7NM_000257.2 c.3523C>TArg1175Trp5probably damagingdeleterious-0.46628.6RCV000536882VUSBKJ1 BKJ21TTNNM_133378.4:c.95123G>AArg31708Gln11probably damaging-5.623.7RCV000172160VUSDJ1 DJ21MYPNNM_032578.3:c.3205C>TArg1069Cys3probably damagingdeleterious5.1635 not reportednaE2 E31EYA4NM_004100.4 c.1294G>CVal432Leu6possibly damagingdeleterious5.424.1RCV000150687VUSEX11TTNNM_133378.4:c.85930G>AGlu28644Lys2possibly damaging-5.9223.7RCV000172194VUSGB11ACTN2NM_001103.3 c.1748A>CGlu583Ala5benigntolerated5.0819.77 not reportednaJR11ACTN2NM_001103.3 c.983G>AArg328Gln4possibly damagingtolerated5.5126.6RCV000293437 RCV000329665VUSLE11TTNNM_133378.4:c.11846G>AGly3949Glu2probably damaging-5.7922 not reportednaLU11MYL2NM_000432.3 c.64G>AGlu22Lys5probably damagingdeleterious4.4433RCV000234985 RCV000015109 RCV000211732 RCV000158914VUS Pathogenic LPMJ11DSG2NM_001943.3 c.2969G>AArg990Lys0possibly damagingdeleterious3.3518.27 not reportednaNB11TTNNM_133378.4:c.94694T>CIle31565Thr12benign-5.4818.11 not reportednaNB11TTNNM_133378.4:c.17C>TPro6Leu5probably damaging-6.1723.8RCV000152540VUSNG11MYH6NM_002471.3 c.4241C>TSer1414Phe0probably damagingdeleterious4.6428RCV000201880VUSNG11TTNNM_133378.4:c.44429T>APhe14810Tyr0probably damaging-5.6416.48 not reportednaPM11TTNNM_133378.4:c.57389G>TArg19130Leu9probably damaging-6.0823.7RCV000205027 RCV000184724VUSPT11FLNCNM_001458.4:c.7561G>AGly2521Ser2probably damagingdeleterious5.5134 not reportednaPT11TTNNM_133378.4:c.100019T>CIle33340Thr8probably damaging-6.0619.63 not reportednaXC11TTNNM_003319.4:c.10432G>AVal3478Ile5probably damaging-6.0722 not reportednaZH11TTNNM_133378.4:c.19619C>TThr6540Met1possibly damaging-5.0118.67 not reportednaACC12TTNNM_133378.4:c.88264G>AVal29422Met10possibly damaging-5.322.2RCV000152176VUSBNR12NEXNNM_144573.3:c.1053+1G>AAbolish splice donor9nana5.1725.8RCV000208507 RCV000041156VUSBOI12TTNNM_133378.4:c.44429T>APhe14810Tyr0probably damaging-5.6416.48 not reportednaDH12LAMA4NM_002290.4:c.3829A>GIle1277Val2benigntolerated0.4428.212 not reportednaDH12FLNCNM_001458.4:c.6403A>GLys2135Glu0benigndeleterious5.2424.1 not reportednaDH12TTNNM_133378.4:c.91550G>AArg30517His12probably damaging-5.8724.2 not reportednaKM12FLNCNM_001458.4:c.2329A>GThr777Ala1possibly damagingdeleterious5.5223.4 not reportednaKM12CALR3NM_145046.4 c.838A>TMet280Leu1benigndeleterious1.8814.24 not reportednab) Double heterozygous variants of uncertain clinical significance in autosomal recessive disease genesFamilyPatient CohortGenecDNA changeConsequencegnomAD allele countPolyPhen HumDivSIFTGERPCADDClinvar IDClinvar ClassificationTF11NDUFS2NM_004550.4:c.329A>TAsp110Val8possibly damagingdeleterious6.0324.2 not reportednaTF11NDUFS2NM_004550.4:c.968G>AArg323Gln1317benigntolerated-0.04517.05RCV000224386 RCV000198518Likely benignZH12ACADVLNM_000018.3:c.325G>AVal109Met6benigndeleterious4.7623.2 not reportedna?ZH12ACADVLNM_000018.3:c.1844G>AArg615Gln746benigntolerated0.88515.27 not reportednac) Mitochondrial genome variants of uncertain clinical significanceFamilyPatient CohortLocusRevised Cambridge Reference Sequence PositionConsequenceGenBank allele count n=37,545Conservation (%)Sequence read depth (Ref, alt)AB11ND13349non-syn:I=>V8243,395ACU1 ACU21ND14132non-syn:A=>T7135,319; 0,292ZH11COX28133non-syn:T=>I182162,210PM11ATP69022non-syn:A=>T71000,274 ................
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