IIHG Clinical Exome Sequencing Test Gene Coverage • Whole Exome Sequencing is a targeted capture platform which does not capture the entire exome. Regions not captured by the exome will not be analyzed. o Please note, it is important to understand the absence of a reportable variant in a given gene does not mean there are not pathogenic variants in that gene. • Data sensitivity and specificity for exome testing is variable as gene coverage is not uniform throughout the exome. • The Agilent SureSelect XT Human All Exon v5 kit captures ~98% of Refseq coding base pairs, and >94% of the captured coding bases in the exome are covered at our depth-of-coverage minimum threshold (30 reads). • All test reports include the following information: o Regions of the Symptom Candidate Gene List which were not captured by the current exome capture platform. o Regions of the Symptom Candidate Gene List which were not sequenced to a sufficient depth of coverage to make a clinical diagnosis. • You can check if genes are captured by the Agilent Agilent SureSelect v5 exome capture, and how well those genes are typically covered here. • Explanations for the headings; • Symbol: Gene symbol • Chr: Chromosome • % Captured: the minimum portion of the gene captured by the Agilent SureSelect XT Human All Exon v5 kit. This includes all transcripts for a given gene. o 100.00% = the entire gene is captured o 0.00% = none of the gene is captured • % Covered: the minimum portion of the gene that has at least 30x average coverage when sequenced on the Illumina HiSeq2000 with 100 base pair (bp) paired-end reads for eight CEPH samples. This is the result for a typical sample, but the minimum when considering all of the different isoforms for the given gene. • % High Quality: The minimum portion of the gene we would anticipate being captured and having 30x sequence coverage or greater. o For example, for the gene BAGE4, 94.26% of the gene is captured, 99.89% of the captured regions of the gene are covered by 30x sequencing depth, for a minimum of 94.15% of BAGE4 will be captured and sequenced to a depth required to make a clinical diagnosis. o Please note, these are minimum values, and any gene may be better covered than the values listed in this table. • Please contact us if you have any questions regarding gene capture and coverage metrics at [email protected]. Symbol Chr % Captured % Covered % High Quality A1BG chr19 100.00% 97.40% 97.40% A1BG-AS1 chr19 100.00% 99.63% 99.63% A1CF chr10 100.00% 99.55% 99.55% A2M chr12 100.00% 96.69% 96.69% A2M-AS1 chr12 100.00% 99.95% 99.95% A2ML1 chr12 100.00% 94.48% 94.48% A2MP1 chr12 100.00% 100.00% 100.00% A3GALT2 chr1 100.00% 98.14% 98.14% A4GALT chr22 100.00% 99.81% 99.81% A4GNT chr3 100.00% 97.17% 97.17% AA06 chr17 100.00% 100.00% 100.00% AAAS chr12 100.00% 97.45% 97.45% AACS chr12 100.00% 98.54% 98.54% AACSP1 chr5 100.00% 100.00% 100.00% AADAC chr3 100.00% 98.79% 98.79% AADACL2 chr3 100.00% 99.48% 99.48% AADACL3 chr1 100.00% 99.63% 99.63% AADACL4 chr1 100.00% 98.76% 98.76% AADACP1 chr3 100.00% 100.00% 100.00% AADAT chr4 100.00% 95.73% 95.73% AAED1 chr9 100.00% 76.58% 76.58% AAGAB chr15 100.00% 98.52% 98.52% AAK1 chr2 100.00% 99.36% 99.36% AAMDC chr11 100.00% 98.53% 98.53% AAMP chr2 100.00% 98.63% 98.63% AANAT chr17 100.00% 88.37% 88.37% AAR2 chr20 100.00% 99.05% 99.05% AARD chr8 100.00% 98.12% 98.12% AARS chr16 100.00% 98.28% 98.28% AARS2 chr6 100.00% 97.64% 97.64% AARSD1 chr17 100.00% 97.24% 97.24% AASDH chr4 100.00% 98.22% 98.22% AASDHPPT chr11 100.00% 99.04% 99.04% AASS chr7 100.00% 98.87% 98.87% AATF chr17 100.00% 98.54% 98.54% AATK chr17 100.00% 94.42% 94.42% AATK-AS1 chr17 100.00% 100.00% 100.00% ABAT chr16 100.00% 98.67% 98.67% ABCA1 chr9 100.00% 95.84% 95.84% ABCA10 chr17 100.00% 94.92% 94.92% ABCA11P chr4 100.00% 99.95% 99.95% ABCA12 chr2 100.00% 97.25% 97.25% ABCA13 chr7 100.00% 98.03% 98.03% ABCA17P chr16 100.00% 100.00% 100.00% ABCA2 chr9 100.00% 96.71% 96.71% ABCA3 chr16 100.00% 95.73% 95.73% ABCA4 chr1 100.00% 96.86% 96.86% ABCA5 chr17 100.00% 97.06% 97.06% ABCA6 chr17 100.00% 92.82% 92.82% ABCA7 chr19 100.00% 96.31% 96.31% ABCA8 chr17 100.00% 96.03% 96.03% ABCA9 chr17 100.00% 97.09% 97.09% ABCB1 chr7 100.00% 97.40% 97.40% ABCB10 chr1 100.00% 81.69% 81.69% ABCB11 chr2 100.00% 97.59% 97.59% ABCB4 chr7 100.00% 95.85% 95.85% ABCB5 chr7 100.00% 97.98% 97.98% ABCB6 chr2 100.00% 98.16% 98.16% ABCB7 chrX 100.00% 94.01% 94.01% ABCB8 chr7 100.00% 98.96% 98.96% ABCB9 chr12 100.00% 97.46% 97.46% ABCC1 chr16 100.00% 96.41% 96.41% ABCC10 chr6 100.00% 96.17% 96.17% ABCC11 chr16 100.00% 96.76% 96.76% ABCC12 chr16 100.00% 97.31% 97.31% ABCC13 chr21 100.00% 100.00% 100.00% ABCC2 chr10 100.00% 98.08% 98.08% ABCC3 chr17 100.00% 95.51% 95.51% ABCC4 chr13 100.00% 96.21% 96.21% ABCC5 chr3 100.00% 98.19% 98.19% ABCC5-AS1 chr3 100.00% 100.00% 100.00% ABCC6 chr16 94.64% 95.95% 90.58% ABCC6P1 chr16 100.00% 100.00% 100.00% ABCC6P2 chr16 100.00% 100.00% 100.00% ABCC8 chr11 100.00% 96.05% 96.05% ABCC9 chr12 100.00% 97.76% 97.76% ABCD1 chrX 93.86% 81.03% 74.89% ABCD2 chr12 100.00% 99.43% 99.43% ABCD3 chr1 100.00% 90.26% 90.26% ABCD4 chr14 100.00% 97.31% 97.31% ABCE1 chr4 100.00% 87.28% 87.28% ABCF1 chr6 100.00% 96.94% 96.94% ABCF2 chr7 100.00% 97.92% 97.92% ABCF3 chr3 100.00% 97.84% 97.84% ABCG1 chr21 100.00% 96.78% 95.77% ABCG2 chr4 100.00% 98.26% 98.26% ABCG4 chr11 100.00% 98.91% 98.91% ABCG5 chr2 100.00% 98.61% 98.61% ABCG8 chr2 100.00% 94.96% 94.96% ABHD1 chr2 100.00% 98.83% 98.83% ABHD10 chr3 100.00% 99.62% 99.62% ABHD11 chr7 100.00% 98.23% 98.23% ABHD11-AS1 chr7 100.00% 100.00% 100.00% ABHD12 chr20 100.00% 88.30% 88.30% ABHD12B chr14 100.00% 90.49% 90.49% ABHD13 chr13 100.00% 99.96% 99.96% ABHD14A chr3 100.00% 92.49% 92.49% ABHD14A-ACY1 chr3 100.00% 91.70% 91.70% ABHD14B chr3 100.00% 97.94% 97.94% ABHD15 chr17 100.00% 96.50% 96.50% ABHD16A chr6 100.00% 94.84% 94.84% ABHD16B chr20 100.00% 99.83% 99.83% ABHD17A chr19 79.42% 64.60% 44.02% ABHD17B chr9 100.00% 99.64% 99.64% ABHD17C chr15 100.00% 88.70% 88.70% ABHD2 chr15 100.00% 99.53% 99.53% ABHD3 chr18 100.00% 98.93% 98.93% ABHD4 chr14 100.00% 99.11% 99.11% ABHD5 chr3 100.00% 99.72% 99.72% ABHD6 chr3 100.00% 96.94% 96.94% ABHD8 chr19 100.00% 98.36% 98.36% ABI1 chr10 100.00% 98.80% 98.80% ABI2 chr2 100.00% 99.33% 99.33% ABI3 chr17 100.00% 93.56% 93.56% ABI3BP chr3 100.00% 96.16% 96.16% ABL1 chr9 100.00% 99.35% 99.35% ABL2 chr1 100.00% 91.21% 91.21% ABLIM1 chr10 100.00% 99.23% 99.23% ABLIM2 chr4 100.00% 97.94% 97.94% ABLIM3 chr5 100.00% 98.36% 98.36% ABO chr9 100.00% 98.00% 98.00% ABR chr17 100.00% 95.16% 95.16% ABRA chr8 100.00% 99.71% 99.71% ABRACL chr6 100.00% 99.66% 99.66% ABT1 chr6 100.00% 98.87% 98.87% ABTB1 chr3 100.00% 96.37% 96.37% ABTB2 chr11 100.00% 96.22% 96.22% ACAA1 chr3 100.00% 92.62% 92.62% ACAA2 chr18 100.00% 70.01% 70.01% ACACA chr17 100.00% 97.91% 97.91% ACACB chr12 100.00% 96.59% 96.59% ACAD10 chr12 100.00% 97.71% 97.71% ACAD11 chr3 100.00% 98.19% 98.19% ACAD8 chr11 100.00% 98.62% 98.62% ACAD9 chr3 100.00% 97.06% 97.06% ACADL chr2 100.00% 94.42% 94.42% ACADM chr1 100.00% 94.68% 94.68% ACADS chr12 100.00% 97.77% 97.77% ACADSB chr10 100.00% 97.75% 97.75% ACADVL chr17 100.00% 95.28% 95.28% ACAN chr15 100.00% 97.48% 97.48% ACAP1 chr17 100.00% 96.92% 96.92% ACAP2 chr3 100.00% 98.74% 98.74% ACAP3 chr1 100.00% 95.05% 95.05% ACAT1 chr11 100.00% 97.96% 97.96% ACAT2 chr6 100.00% 98.48% 98.48% ACBD3 chr1 100.00% 99.34% 99.34% ACBD4 chr17 100.00% 94.81% 94.81% ACBD5 chr10 100.00% 98.42% 98.42% ACBD6 chr1 100.00% 97.29% 97.29% ACBD7 chr10 100.00% 99.53% 99.53% ACCS chr11 100.00% 92.35% 92.35% ACCSL chr11 100.00% 97.50% 97.50% ACD chr16 100.00% 97.39% 97.39% ACE chr17 100.00% 93.68% 93.68% ACE2 chrX 100.00% 97.65% 97.65% ACER1 chr19 100.00% 98.87% 98.87% ACER2 chr9 100.00% 99.24% 99.24% ACER3 chr11 100.00% 95.49% 95.49% ACHE chr7 100.00% 90.82% 90.82% ACIN1 chr14 100.00% 97.58% 97.58% ACKR1 chr1 100.00% 99.84% 99.84% ACKR2 chr3 100.00% 99.90% 99.90% ACKR3 chr2 100.00% 99.72% 99.72% ACKR4 chr3 100.00% 99.96% 99.96% ACLY chr17 100.00% 97.35% 97.35% ACMSD chr2 100.00% 97.11% 97.11% ACN9 chr7 100.00% 99.90% 99.90% ACO1 chr9 100.00% 98.54% 98.54% ACO2 chr22 100.00% 84.08% 84.08% ACOT1 chr14 100.00% 57.44% 57.44% ACOT11 chr1 100.00% 88.88% 88.88% ACOT12 chr5 100.00% 91.63% 91.63% ACOT13 chr6 100.00% 99.85% 99.85% ACOT2 chr14 100.00% 92.59% 92.59% ACOT4 chr14 100.00% 91.88% 91.88% ACOT6 chr14 100.00% 99.41% 99.41% ACOT7 chr1 100.00% 96.57% 96.57% ACOT8 chr20 100.00% 98.05% 98.05% ACOT9 chrX 100.00% 96.40% 96.40% ACOX1 chr17 100.00% 99.50% 99.50% ACOX2 chr3 100.00% 96.18% 96.18% ACOX3 chr4 100.00% 97.68% 97.68% ACOXL chr2 100.00% 97.30% 97.30% ACP1 chr2 100.00% 90.88% 90.88% ACP2 chr11 100.00% 95.06% 95.06% ACP5 chr19 100.00% 96.52% 96.52% ACP6 chr1 100.00% 91.46% 91.46% ACPP chr3 100.00% 98.14% 98.14% ACPT chr19 100.00% 82.09% 82.09% ACR chr22 100.00% 90.49% 90.49% ACRBP chr12 100.00% 98.49% 98.49% ACRC chrX 100.00% 98.25% 98.25% ACRV1 chr11 100.00% 99.21% 99.21% ACSBG1 chr15 100.00% 97.75% 97.75% ACSBG2 chr19 100.00% 98.64% 98.64% ACSF2 chr17 100.00% 98.25% 98.25% ACSF3 chr16 100.00% 98.86% 98.86% ACSL1 chr4 100.00% 97.91% 97.91% ACSL3 chr2 100.00% 98.46% 98.46% ACSL4 chrX 100.00% 96.66% 96.66% ACSL5 chr10 100.00% 97.49% 97.49% ACSL6 chr5 100.00% 98.47% 98.47% ACSM1 chr16 100.00% 94.91% 94.91% ACSM2A chr16 100.00% 99.13% 99.13% ACSM2B chr16 100.00% 98.86% 98.86% ACSM3 chr16 100.00% 98.90% 98.90% ACSM4 chr12 100.00% 92.15% 92.15% ACSM5 chr16 100.00% 91.21% 91.21% ACSM6 chr10 100.00% 98.03% 98.03% ACSS1 chr20 100.00% 94.10% 94.10% ACSS2 chr20 100.00% 89.49% 89.49% ACSS3 chr12 100.00%