Perkinelmer Genomics to Request the Saliva Swab Collection Kit for Patients That Cannot Provide a Blood Sample As Whole Blood Is the Preferred Sample

STAT Focused Autism and Intellectual Disability Panel

Test Code D5130F

Test Summary This test analyzes 264 genes that have been associated with Autism and Intellectual Disability. STAT means results are available in 7 - 10 days.

Turn-Around-Time (TAT)* 7 - 10 days

Acceptable Sample Types Whole Blood (EDTA) (Preferred sample type) DNA, Isolated Dried Blood Spots Saliva

Acceptable Billing Types Self (patient) Payment Institutional Billing

Indications for Testing

This panel may be appropriate for individuals with a clinical suspicion of Lissencephaly and/or for indiviudals with a family history of Lissencephaly.

Test Description

This panel analyzes 264 genes that have been associated with Focused Autism and Intellectual Disability and/or disorders associated with Focused Autism and Intellectual Disability. Both sequencing and deletion/duplication (CNV) analysis will be performed on the coding regions of all genes included (unless otherwise marked). All analysis is performed utilizing Next Generation Sequencing (NGS) technology. CNV analysis is designed to detect the majority of deletions and duplications of three exons or greater in size. Smaller CNV events may also be detected and reported, but additional follow-up testing is recommended if a smaller CNV is suspected. All variants are classified according to ACMG guidelines.

Condition Description

Autism Spectrum Disorder (ASD) refers to a group of developmental disabilities that are typically associated with challenges of varying severity in the areas of social interaction, communication, and repetitive/restricted behaviors. Autism is a brain disorder that typically appears during the first three years of life.

Genes

ADNP, ADSL, AFF2, AHDC1, AKAP9, ALDH5A1, ALDH7A1, ALG6, AMT, ANK2, ANKRD11, ANXA1, AP1S2, AP3B2, AP4B1, ARFGEF2, ARID1B, ARID2, ARX, ASAH1, ASH1L, ASPM, ASXL1, ASXL3, ATP10A, ATP1A3, ATRX, AUTS2, BCKDK, BCL11A, BRAF, BRAT1, C5orf42, CACNA1C, CACNA1D, CACNA1E, CACNA1H, CASK, CBL, CC2D1A, CDC42BPB, CDKL5, CEP135, CHAMP1, CHD2, CHD7, CHD8, CHKB, CHMP1A, CIB2, CIC, CNTNAP2, CREBBP, CSMD1, CTCF, CTNNA3, CTNNB1, CUL3, CYP27A1, DDX3X, DEAF1, DHCR7, DLG2, DMD, DNMT3A, DPP6, DPYD, DYNC1H1, DYRK1A, EBF3, EFR3A, EFTUD2, EHMT1, ELOVL4, ELP4, EP300, ERCC6, FBXL4, FGD1, FMR1, FOLR1, FOXG1, FOXP1, FOXP2, GATAD2B, GATM, GPC4, GPHN, GRIA1, GRIK2, GRIN1, GRIN2B, HCN1, HDAC8, HECW2, HEPACAM, HERC2, HIVEP2, HNRNPU, HPRT1, IL1RAPL1, IQSEC2, ITPR1, ITSN1, KANSL1, KAT6A, KAT6B, KATNAL2, KCNB1, KCNJ10, KCNQ2, KCNQ3, KDM5B, KDM5C, KDM6A, KDM6B, KIAA2022, KIF11, KMT2A, KMT2C, KMT2D, L1CAM, LAMA2, LAMB1, LARP7, LRP2, MAGEL2, MBD5, MECP2, MED12, MED13, MED13L, MEF2C, MET, MID1, MTOR, MYH10, MYO5A, MYT1L, NALCN, NAV2, NBEA, NCKAP1, NEDD9, NFIA, NFIX, NGLY1, NHS, NIPBL, NLGN1, NLGN3, NLGN4X, NR1I3, NRXN1, NSD1, NSUN2, OCRL, OPHN1, OXTR, PACS1, PAFAH1B1, PAH, PARK2, PAX5, PAX6, PCCA, PCCB, PCDH19, PDHA1, PER2, PGAP1, PHF2, PHF21A, PHF6, PHIP, PIK3R2, PLA2G6, PNKP, POGZ, PON1, PQBP1, PRICKLE2, PRKD1, PRODH, PTCHD1, PTEN, PTPN11, PURA, RAB39B, RAI1, RELN, RIMS1, ROBO2, SATB2, SBF1, SCN1A, SCN2A, SCN9A, SEMA5A, SETBP1, SETD1A, SETD2, SETD5, SGSH, SHANK1, SHANK2, SHANK3, SLC12A5, SLC2A1, SLC35A2, SLC6A1, SLC6A3, SLC6A8, SLC7A3, SLC9A6, SMAD4, SMARCA2, SMARCA4, SMARCB1, SMC1A, SON, SOX11, SOX5, SPAST, SPEN, SPP2, SRCAP, STAG1, STXBP1, SURF1, SYNGAP1, TAF1, TAF6, TBL1XR1, TBR1, TCF20, TCF4, TCF7L2, TCOF1, TMLHE, TPP1, TRAPPC9, TRIO, TRIP12, TRPC6, TRRAP, TSC1, TSC2, UBE2A, UBE3A, UPF3B, USP9X, VPS13B, WAC, WDFY3, WDR45, WWOX, YTHDC1, YY1, ZBTB18, ZBTB20, ZEB2, ZMYND11, ZWILCH

250 Industry Drive Pittsburgh, PA 15275 • T 866-354-2910 • F 412-220-0785 www.perkinelmergenomics.com Page 1 of 3 Test Methods and Limitations

Sequencing is performed on genomic DNA using an Agilent targeted sequence capture method to enrich for the genes on this panel. Direct sequencing of the amplified captured regions was performed using 2X100bp reads on Illumina next generation sequencing (NGS) systems. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. Low coverage regions, if any, are limited to ~1% or less of the nucleotides in the test unless a pathogenic variant explaining the phenotype is discovered. A list of these regions is available upon request. Alignment to the human reference genome (hg19) is performed and annotated variants are identified in the targeted region. Variants are called at a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Single nucleotide variants (SNVs) meeting internal quality assessment guidelines are confirmed by Sanger sequence analysis for records after results are reported. Indels and SNVs are confirmed by Sanger sequence analysis before reporting at director discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter and enhancer regions, areas containing large numbers of tandem repeats, and variants in mitochondrial DNA. Copy number variation (CNV) analysis is designed to detect deletions and duplications of three exons or more; in some instances, due to the size of the exons or other factors, not all CNVs may be analyzed. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina DRAGEN Bio-IT Platform v.2.03. Secondary and tertiary data analysis is performed using PerkinElmer’s internal ODIN v.1.01 software for SNVs and Biodiscovery’s NxClinical v.4.3 or Illumina DRAGEN Bio-IT Platform v.2.03 for CNV and absence of heterozygosity (AOH).

Detailed Sample Requirements

Whole Blood (EDTA) (Preferred sample type)

Collection Container(s):

EDTA (purple top)

Collection:

Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: 5 to 10 mL Southern Blot Analysis requires 3 mL blood.

Sample Condition: Store at ambient temperature. Do not refrigerate or freeze. Shipping: Ship overnight at ambient temperature ensuring receipt within 4-days of collection.

SPECIAL INSTRUCTIONS: Clotted or hemolyzed samples are not accepted.

DNA, Isolated

Collection: Required DNA Quantity by Test Type*:

Next Generation Sequencing (NGS): Send >500ng total gDNA @ > 15ng/?L. Please ship samples in 10mM Tris. No EDTA. Sanger Sequencing: Send 5 to 25 micrograms (varies by size of gene). Please contact the laboratory for specificamounts. Non-Sequencing Tests: Send 20 micrograms Array-based Tests: Send 10 micrograms

*Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be >= 1.8. Shipping: Ship overnight at ambient temperature.

SPECIAL INSTRUCTIONS:

Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g. proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g. of other family members) may be required to confirm results. Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case

250 Industry Drive Pittsburgh, PA 15275 • T 866-354-2910 • F 412-220-0785 www.perkinelmergenomics.com Page 2 of 3 basis. Please call to speak with a laboratory genetic counselor prior to submitting a DNA sample from any non-CLIA certified laboratory. Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.

Dried Blood Spots

Collection Container(s): Dried blood spot card Collection: Follow kit instructions. Briefly, allow blood to saturate card until indicated areas are filled and blood has soaked through card. Air dry card at ambient temperature for at least 3 hours.

NBS: Please contact PKIG to request the StepOne® kit. Gene Sequencing: Please contact PKIG to request the DBS collection kit.

Shipping: Follow kit instructions. Double bag and ship overnight at ambient temperature.

Saliva

Collection Container(s): ORAcollect®•Dx Saliva Swab Collection Kit Collection: Collect saliva in an ORAcollect®•Dx Saliva Swab Collection Kit according to the manufacturer's instructions. Please contact PerkinElmer Genomics to request the saliva swab collection kit for patients that cannot provide a blood sample as whole blood is the preferred sample. Sample Condition: Store at ambient temperature. Do not refrigerate or freeze. Shipping: Ship overnight at ambient temperature.

250 Industry Drive Pittsburgh, PA 15275 • T 866-354-2910 • F 412-220-0785 www.perkinelmergenomics.com Page 3 of 3