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Autism NGS Panel

Autism NGS Panel

  • Panel Description
  • Test Description
  • CPT Codes
  • Resources

Panel Description

Diseases Targeted:
Autism Spectrum Disorder
Tuberous Sclerosis Complex
Noonan Syndrome
Rett Syndrome
Cornelia de Lange Syndrome
CHARGE Syndrome
Cohen Syndrome
Phelan-McDermid Syndrome
Smith-Lemli-Opitz Syndrome
Sotos Syndrome
PTEN Hamartoma Tumor Syndrome

Overview:
Autism spectrum disorder (ASD) is the collective term for a wide range of conditions characterized by social, behavioral, and communication challenges. Many affected individuals develop symptoms in the first year of life and are diagnosed in the following years. People with ASD may have difficulty with eye contact, responding to change, or communicating. ASD may include sensory sensitivities or other health problems like seizures, sleep difficulties, anxiety, depression, or gastrointestinal (GI) disorders. While there is no cure for ASD, diagnosis and personalized treatment can help with social and behavioral development.

This panel covers over 100 genes with strong evidence-based links to autism. This includes FOXP1, SYNGAP1, CHD8, SCN2A and other significant genes that play a role in the development and expression of neuronal activity. Additionally, the panel includes genes associated with syndromic conditions that include ASD as a feature, such as tuberous sclerosis complex, Smith-Lemli-Opitz syndrome, Sotos syndrome, PTEN hamartoma syndrome, CHARGE syndrome, Cohen syndrome, Noonan syndrome, and Rett syndrome.

Who is this test for?
This panel is recommended for anyone with a personal or family history of ASD. People with unexplained communication problems, behavioral issues, or developmental delays may also benefit.

What are the potential benefits for my patient?
Symptoms of ASD vary from person to person and there may not be any obvious physical symptoms which makes diagnosis difficult. To date, there are no blood tests or other procedures that can confirm a diagnosis. Genetic testing is one of the few ways to establish a diagnosis when the patient’s ASD is linked to genetic factors. Accurate diagnosis can critically help patients who are struggling socially or mentally as it opens doors for more personalized treatment.

Genetic testing for autism can:
  • Establish or confirm the appropriate diagnosis
  • Identify risks for additional  related symptoms
  • Assist in modifying lifestyle changes
  • Result in more personalized treatment and symptom management
  • Inform family members about their own risk factors
  • Connect patients to relevant resources & support
  • Provide options for family planning

Test Description

Print
Order Options:
  • Sequencing
  • Del/Dup
  • Rush / STAT
  • Exclude VUS
  • MCC
  • Duo/Trio
Turnaround Time:
3-5 weeks
Cost:
Call for details
Genes:
ADNP, ALDH5A1, ANK3, ANKRD11, AP1S2, ARHGEF6, ARX, ATP10A, ATRX, AUTS2, AVPR1A, BCL11A, BDNF, BRAF, BRSK2, CACNA1C, CASK, CDKL5, CHD7, CHD8, CIC, CNTNAP2, CNTNAP5, CREBBP, CSNK2A1, DHCR7, DLGAP2, DMD, DOCK4, DPP10, DPP6, DPYD, EHMT1, FAAH2, FGD1, FMR1, FOLR1, FOXG1, FOXP1, FOXP2, GABRB3, GRIN2B, GRPR, GSPT2, HOXA1, HPRT1, HUWE1, IL1RAPL1, IMMP2L, KATNAL2, KCTD13, KDM5C, KIRREL3, KMT5B, L1CAM, LAMC3, MBD5, MECP2, MED12, MEF2C, MET, MID1, NEGR1, NF1, NHS, NIPBL, NLGN3, NLGN4X, NRXN1, NSD1, NSDHL, NTNG1, OCRL, OPHN1, PAFAH1B1, PCDH19, PCDH9, PDE10A, PDE4D, PHF6, PIP5K1B, PNKP, PON3, PQBP1, PTCHD1, PTEN, PTPN11, RAB39B, RAI1, RBFOX1, RELN, RORA, RPL10, RPS6KA3, SATB2, SCN1A, SCN2A, SHANK2, SHANK3, SLC16A2, SLC6A4, SLC9A6, SLC9A9, SMC1A, SMG6, SNRPN, SOX5, SPAST, ST7, STK3, SYNGAP1, TBR1, TCF4, TSC1, TSC2, UBE3A, VPS13B, ZEB2, ZNF507, ZNF804A, ZNHIT6 ( 121 genes )
Coverage:
96% at 20x
Specimen Requirements:
Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in EB buffer) or Buccal Swab or Saliva (kits available upon request)
Test Limitations:
All sequencing technologies have limitations. This analysis is performed by Next Generation Sequencing (NGS) and is designed to examine coding regions and splicing junctions. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the contribution of pseudogene sequences or other highly-homologous sequences, these may still occasionally interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Sanger sequencing is used to confirm variants with low quality scores and to meet coverage standards. If ordered, deletion/duplication analysis can identify alterations of genomic regions which include one whole gene (buccal swab specimens and whole blood specimens) and are two or more contiguous exons in size (whole blood specimens only); single exon deletions or duplications may occasionally be identified, but are not routinely detected by this test. Identified putative deletions or duplications are confirmed by an orthogonal method (qPCR or MLPA). This assay will not detect certain types of genomic alterations which may cause disease such as, but not limited to, translocations or inversions, repeat expansions (eg. trinucleotides or hexanucleotides), alterations in most regulatory regions (promoter regions) or deep intronic regions (greater than 20bp from an exon). This assay is not designed or validated for the detection of somatic mosaicism or somatic mutations.

Gene Specifics:
Gene Notes
MECP2 Currently available technologies (NGS and qPCR) are not amenable to detection of single exon deletions/duplications of exon 1 in the MECP2 gene.
CPT Codes:
CPT Code 81407, 81408, 81479

NOTE:  The CPT codes listed on the website are in accordance with Current Procedural Terminology, a publication of the American Medical Association. CPT codes are provided here for the convenience of our clients. Clients who bill for services should make the final decision on which codes to use.

Resources

DescriptionDownload
Autism Spectrum Disorder