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Cornelia de Lange Syndrome and Cornelia de Lange Syndrome-Related Disorders Sequencing Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
5449 AFF4 81479 Add to Order
ANKRD11 81479
ARHGAP31 81479
ARID1A 81479
ARID1B 81479
CHD7 81407
CREBBP 81407
CTCF 81479
DLL4 81479
DOCK6 81479
EOGT 81479
EP300 81479
ESCO2 81479
HDAC8 81479
KDM1A 81479
KMT2A 81479
MED12 81479
NIPBL 81479
NOTCH1 81408
PHF6 81479
RAD21 81479
RBPJ 81479
SMARCA4 81479
SMARCB1 81479
SMARCE1 81479
SMC1A 81479
SMC3 81479
SOX11 81479
SRCAP 81479
TAF1 81479
TAF6 81479
WDR26 81479
Full Panel Price* $2290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
5449 Genes x (32) $2290.00 81407(x2), 81408, 81479(x29) Add to Order
Pricing Comment

If you would like to order a subset of these genes contact us to discuss pricing.

Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Over 70% of all Cornelia de Lange Syndrome (CdLS) patients harbor a pathogenic variant in NIPBL, SMC3, RAD21, SMC1A, or HDAC8 (Boyle et al. 2015). Only a few patients have been reported with pathogenic variants in AFF4, ANKRD11 and KMT2A. Most CdLS patients reported to date had a de novo pathogenic variant.

This test is expected to detect causative variants in about 60% of patients with Coffin-Siris Syndrome. Most of the patients had a de novo variant in one of the ARID1A, ARID1B, SMARCA4, SMARCB1, SMARCE1, and SOX11 genes (Vergano et al. 2016).

Pathogenic variants in CHD7 were detected in 65% -70% of patients with clinically diagnosed CHARGE syndrome, and most patients had a de novo CHD7 pathogenic variant (Lalani et al. 2012).

Sequence analysis can detect CREBBP pathogenic variants in 40%-50% of Rubinstein-Taybi syndrome cases. Pathogenic variants in EP300 are identified in 3%-8% of patients with Rubinstein–Taybi syndrome (Stevens 2014). 16p13.3 microdeletions (ranging from 3.3kb to 3900kb) involving CREBBP were found 17 out of 83 patients with typical features of Rubinstein–Taybi syndrome using array CGH and quantitative multiplex fluorescent-PCR (Stef et al. 2007).

SRCAP truncating de novo variants were found in 6 out of 9 patients with Floating-Harbor syndrome (Le Goff et al. 2013).

In one study, pathogenic variants in the ESCO2 gene were found in all 17 Roberts syndrome patients who were from 16 unrelated families (Gordillo et al. 2008).

DOCK6 and EOGT pathogenic variants were identified in 2 and 3 of 5 families with autosomal recessive Adams-Oliver syndrome, respectively (Shaheen et al. 2013). DLL4 pathogenic variants were found in 9 of 91 families Adams-Oliver syndrome, one occurred as de novo (Meester et al. 2015). NOTCH1 pathogenic variants explain ~17% of patients with Adams-Oliver syndrome (Southgate et al. 2015). There are almost 80 documented NOTCH1 pathogenic variants: missense ~55%, truncating ~ 26%, splicing ~11% and ~6% large deletion (Human Gene Mutation Database; Stittrich et al. 2014; Southgate et al. 2015).

The majority of unique MED12 pathogenic variants were found in patients with intellectual disability. The MED12 (2881C>T, p.Arg961Trp) variant was found in 13% (6 /45) of studied unrelated FG Syndrome families (Risheg et al. 2007). Almost all documented MED12 pathogenic variants are missense, except one for truncating. No Large deletion/duplications have been reported (Human Gene Mutation Database).

Only 4 truncating ARHGAP31 pathogenic variants were reported to be segregated with disease in four unrelated families (Southgate et al. 2011; Isrie et al. 2014, Human Gene Mutation Database). Only two missense variants in RBPJ were reported to be segregated with disease in two families with with Adams-Oliver syndrome (Hassed et al. 2012).

Only 3 de novo missense KDM1A variants were reported in patients with severe non-syndromic sporadic intellectual disability (Rauch A. et al. 2012) or Kabuki syndrome-like phenotype (Tunovic et al. 2014). One large multiple gene deletion including part of KDM1A was reported in one patient with Li-Fraumeni syndrome with brain tumour (Aury-Landas et al. 2013).

In one study, a de novo KMT2A pathogenic variant was found in one out of 32 Turkish patients clinically diagnosed with Cornelia de Lange syndrome (Yuan et al. 2015). In another study, de novo KMT2A pathogenic variants were found in five of the six Wiedemann-Steiner syndrome patients (Jones et al. 2012).

So far only four de novo unique CTCF pathogenic variants were reported (1 missense, 2 truncating, and 1 large multiple gene deletion involving CTCF) (Gregor A. et al. 2013; Human Gene Mutation Database).

To date, more than 10 unique TAF1 pathogenic variants were reported; almost all of them are missense, except for one splicing, and 2 large duplications involving TAF1, de novo variants were found in ~50% of the studied patients/families (O'Rawe J.A. et al. 2015).

So far, only three rare missense variants (2 of them are de novo) in the WDR26 gene were reported in two patient with Long QT syndrome (Shigemizu et al. 2015) and one patient with autism spectrum disorder (Wang et al. 2016).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 ANKRD11$690.00 81479 Add to Order
ARHGAP31$690.00 81479
ARID1A$690.00 81479
ARID1B$690.00 81479
CHD7$690.00 81479
CREBBP$690.00 81406
CTCF$690.00 81479
EP300$690.00 81479
ESCO2$690.00 81479
MED12$690.00 81479
NIPBL$690.00 81479
NOTCH1$690.00 81479
PHF6$690.00 81479
RBPJ$690.00 81479
SMARCA4$690.00 81479
SMARCB1$690.00 81479
SMARCE1$690.00 81479
SMC1A$690.00 81479
SMC3$690.00 81479
SRCAP$690.00 81479
Full Panel Price* $1290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (20) $1290.00 81406, 81479(x19) Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Intragenic NIPBL deletions and a duplication were identified in 13 (2.5%) out of 510 CdLS cases (12 deletions and 1 duplication) (Cheng et al. 2014). Large deletions and duplications account for 11% of reported SMC1A pathogenic variants (Gilissen et al. 2014; Baquero-Montoya et al. 2014). Large deletion/duplication account for ~30% of reported pathogenic variants in the ANKRD11 gene (Human Gene Mutation Database).

Large pathogenic CHD7 deletions have been reported in less than 5% of patients with a clinical diagnosis of CHARGE syndrome (Bergman et al. 2008; Wincent et al. 2009; Blake et al. 2011).

In one study, a large deletion involving SOX11 was reported in 7 of 10 studied Coffin–Siris syndrome patients (Hempel et al. 2016).

Large deletions/duplications account for ~20% documented pathogenic variants in the ARID1B gene (Human Gene Mutation Database). For example, diffierent sized heterozygous large de novo deletions involving ARID1B were reported in 7 patients with clinical features of corpus callosum defects, intellectual disability, speech impairment, and autism (Halgren et al. 2012).

A large deletion involving NOTCH1 accounts for ~6% of documented NOTCH1 pathogenic variants (Human Gene Mutation Database; Stittrich et al. 2014; Southgate et al. 2015).

16p13.3 microdeletions (ranging from 3.3kb to 3900kb) involving CREBBP were found 17 out of 83 patients with typical features of Rubinstein–Taybi syndrome using array CGH and quantitative multiplex fluorescent-PCR (Stef et al. 2007).

One large deletion in EP300 was found in 1 of 33 Rubinstein-Taybi syndrome patients (Negri et al. 2015).

Only a few deletion/duplications were reported in the ARID1A, CTCF, KDM1A, KMT2A, PHF6, SMARCA4, SMARCE1, SRCAP, and TAF1 genes.

No large deletion/duplications have been reported in the following genes: ARHGAP31, ESCO2, MED12, RBPJ, and SMC3.

Deletion and duplication testing is currently unavailable for the AFF4, DLL4, DOCK6, EOGT, HDAC8, KDM1A, KMT2A, RAD21, SOX11, TAF1, TAF6, and WDR26 genes.

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Clinical Features

This panel includes genes currently known to be associated with Cornelia de Lange syndrome, Adams-Oliver syndrome, Coffin-Siris syndrome, CHARGE syndrome, Floating-Harbor syndrome, Rubinstein-Taybi syndrome, Roberts syndrome, FG Syndrome (also known as Opitz-Kaveggia Syndrome), Wiedemann-Steiner syndrome, KDM1A –related cleft palate, psychomotor retardation, and distinctive facial features, as well as intellectual disability related to CTCF, TAF1and WDR26. For clinical and genetic information, please see individual gene test descriptions on our website or visit https://omim.org.

Genetics

Cornelia de Lange syndrome (CdLS): NIPBL, SMC3, RAD21, KMT2A, AFF4 and ANKRD11-related CdLS are all inherited in autosomal dominant manner, while SMC1A and HDAC8-related CdLS are inherited in an X-linked manner. Female carriers of SMC1A and HDAC8 pathogenic variants may show variable symptoms depending on random X-inactivation. TAF6 variants were reported to be related to autosomal recessive CdLS.

Adams-Oliver syndrome: Pathogenic variants in ARHGAP31, DLL4, NOTCH1 and RBPJ cause autosomal dominant Adams-Oliver syndrome, while pathogenic variants in DOCK6 and EOGT cause autosomal recessive Adams-Oliver syndrome.

CHARGE syndrome is autosomal dominant condition caused by pathogenic variants in the CHD7 gene.

Coffin-Siris syndrome: ARID1A, ARID1B, SMARCA4, SMARCB1, SMARCE1, and SOX11 related Coffin-Siris syndrome are inherited in an autosomal dominant manner. PHF6 pathogenic variants mainly cause X-linked Börjeson-Forssman-Lehmann syndrome. Recently, two large deletions involving part or whole PHF6 were reported to be causative for X-linked Coffin-Siris syndrome.

KDM1A –related cleft palate, psychomotor retardation, and distinctive facial features is inherited in an autosomal dominant manner.

Floating-Harbor syndrome is inherited in an autosomal dominant manner caused by pathogenic variants in the SRCAP gene.

Lujan syndrome (also known as Lujan-Fryns Syndrome) and FG syndrome Type 1 (also known as Opitz-Kaveggia Syndrome) and Ohdo syndrome, MKB type are inherited in an X-linked recessive manner and cased by pathogenic variants in the MED12 gene.

Roberts syndrome is inherited in autosomal recessive manner caused by pathogenic variants in the ESCO2 gene.

Rubinstein-Taybi syndrome is inherited in an autosomal dominant manner caused by pathogenic variants in the CREBBP and EP300 genes.

Wiedemann-Steiner syndrome is inherited in an autosomal dominant manner and caused by pathogenic variant in the KMT2A gene.

Pathogenic variants in TAF1 were mainly found in male patients with X-linked dysmorphic features, intellectual disability & neurological manifestations (O'Rawe J.A. et al. 2015).

Pathogenic variants in CTCF cause autosomal dominant intellectual disability.

WDR26 was reported to be associated with autism spectrum disorder.

See individual gene test descriptions for information on molecular biology of gene products.

Testing Strategy

For this Next Generation Sequencing (NGS) test, sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for regions not captured or with insufficient number of sequence reads. All reported pathogenic, likely pathogenic, and variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, polymerase chain reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

This panel provides full coverage of all coding exons of the genes listed, plus ~20 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads for coding regions and 0-10 bases of flanking DNA, >10X NGS reads for 11-20 bases of flanking DNA, or Sanger sequencing.

Indications for Test

Candidates for this test are patients with clinical features of Cornelia de Lange syndrome, Adams-Oliver syndrome, Coffin-Siris syndrome, CHARGE syndrome, Floating-Harbor syndrome, Rubinstein-Taybi syndrome, Roberts syndrome, FG Syndrome (also known as Opitz-Kaveggia Syndrome), Wiedemann-Steiner syndrome, KDM1A–related cleft palate, psychomotor retardation, and distinctive facial features, as well as intellectual disability related to CTCF, TAF1 and WDR26.

Diseases

Name Inheritance OMIM ID
Adams-Oliver Syndrome 1 AD 100300
Adams-Oliver Syndrome 2 AR 614219
Adams-Oliver Syndrome 3 AD 614814
Adams-Oliver Syndrome 4 AR 615297
Adams-Oliver Syndrome 5 AD 616028
Adams-Oliver Syndrome 6 AD 616589
Alazami-Yuan Syndrome AR 617126
Borjeson-Forssman-Lehmann Syndrome AR 301900
CHARGE Association AD 214800
CHOPS Syndrome AD 616368
Cleft Palate, Psychomotor Retardation, and Distinctive Facial Features AD 616728
Coffin-Siris Syndrome 1 AD 135900
Coffin-Siris Syndrome 2 AD 614607
Coffin-Siris Syndrome 3 AD 614608
Coffin-Siris Syndrome 4 AD 614609
Coffin-Siris Syndrome 5 AD 616938
Cornelia de Lange syndrome 1 AD 122470
Cornelia de Lange syndrome 2 XL 300590
Cornelia de Lange syndrome 3 AD 610759
Cornelia de Lange syndrome 4 AD 614701
Cornelia de Lange syndrome 5 XL 300882
Fg Syndrome XLR 305450
Floating-Harbor Syndrome AD 136140
KBG Syndrome AD 148050
Lujan-Fryns Syndrome XLR 309520
Mental Retardation, Autosomal Dominant 21 AD 615502
Mental Retardation, Autosomal Dominant, 27 AD 615866
Mental Retardation, X-linked, Syndromic 33 XLR 300966
OHDO Syndrome, X-linked; OHDOX XLR 300895
Rhabdoid Tumor Predisposition Syndrome 2 AD 613325
Roberts Syndrome AR 268300
Roberts-SC Phocomelia Syndrome AR 269000
Rubinstein-Taybi Syndrome AD 180849
Rubinstein-Taybi Syndrome 2 AD 613684
Wiedemann-Steiner Syndrome AD 605130

Related Tests

Name
Adams-Oliver Syndrome via the DOCK6 Gene
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
CHARGE and Kallmann Syndromes Sequencing Panel
CHARGE and Kallmann Syndromes via the CHD7 Gene
CHARGE Syndrome via the SEMA3E Gene
CHOPS Syndrome via the AFF4 Gene
Coffin-Siris Syndrome Sequencing Panel
Comprehensive Cardiology Sequencing Panel with CNV Detection
Congenital Abnormalities of the Kidney and Urinary Tract (CAKUT) Sequencing Panel with CNV Detection
Cornelia de Lange Syndrome and Wiedemann-Steiner Syndrome via the KMT2A Gene
Cornelia de Lange Syndrome Sequencing Panel
Cornelia de Lange Syndrome via the ANKRD11 Gene
Cornelia de Lange Syndrome via the HDAC8 Gene
Cornelia de Lange Syndrome via the NIPBL Gene
Cornelia de Lange Syndrome via the RAD21 Gene
Cornelia de Lange Syndrome via the SMC1A Gene
Cornelia de Lange Syndrome via the SMC3 Gene
Disorders of Sex Development and Infertility Sequencing Panel with CNV Detection
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Female Infertility Sequencing Panel with CNV Detection
Floating-Harbor Syndrome via the SRCAP Gene
Hereditary Breast and Ovarian Cancer Syndrome - HBOC EXPANDED Sequencing and Deletion/Duplication Panel
Lujan Syndrome, FG Syndrome Type 1 and Ohdo Syndrome via the MED12 Gene
Male Infertility Sequencing Panel with CNV Detection
Marfan Syndrome and Related Aortopathies Sequencing Panel
Non-syndromic Intellectual Disability (NS-ID) Sequencing Panel with CNV Detection
Ovarian Cancer and Rhabdoid Tumor Predisposition Syndrome via the SMARCA4 Gene
Parkinson Disease Sequencing Panel
Renal Cancer Sequencing Panel
Rhabdoid Tumor Predisposition Syndrome via the SMARCB1 Gene
Roberts Syndrome via the ESCO2 Gene
Rubinstein-Taybi Syndrome and Floating-Harbor Syndrome Sequencing Panel
Rubinstein-Taybi Syndrome via the CREBBP Gene
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CONTACTS

Genetic Counselors
Geneticist
Citations
  • Aury-Landas J. et al. 2013. European Journal of Human Genetics. 21: 1369-76. PubMed ID: 23612572
  • Baquero-Montoya C. et al. 2014. Clinical Genetics. 85: 446-51. PubMed ID: 23683030
  • Bergman J.E. et al. 2008. European Journal of Medical Genetics. 51: 417-25. PubMed ID: 18472328
  • Boyle M.I. et al. 2015. Clinical Genetics. 88: 1-12. PubMed ID: 25209348
  • Cheng Y.W. et al. 2014. Molecular Genetics & Genomic Medicine. 2: 115-23. PubMed ID: 24689074
  • Gilissen C. et al. 2014. Nature. 511: 344-7. PubMed ID: 24896178
  • Gordillo M. et al. 2008. Human Molecular Genetics. 17: 2172-80. PubMed ID: 18411254
  • Gregor A. et al. 2013. American Journal of Human Genetics. 93: 124-31. PubMed ID: 23746550
  • Halgren C. et al. 2012. Clinical Genetics. 82: 248-55. PubMed ID: 21801163
  • Hassed SJ. et al. 2012. American journal of human genetics. 91: 391-5. PubMed ID: 22883147
  • Hempel A. et al. 2016. Journal of Medical Genetics. 53: 152-62. PubMed ID: 26543203
  • Human Gene Mutation Database (Bio-base).
  • Isrie M. et al. 2014. American Journal of Human Genetics. 164A: 1576-9. PubMed ID: 24668619
  • Jones W.D. et al. 2012. American Journal of Human Genetics. 91: 358-64. PubMed ID: 22795537
  • Lalani S.R. et al. 2012. CHARGE Syndrome.In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301296
  • Le Goff C. et al. 2013. Human Mutation. 34: 88-92.
  • Meester J.A. et al. 2015. American Journal of Human Genetics. 97: 475-82. PubMed ID: 26299364
  • Negri G. et al. 2015. Clinical Genetics. 87: 148-54. PubMed ID: 24476420
  • O'Rawe J.A. et al. 2015. American Journal of Human Genetics. 97: 922-32. PubMed ID: 26637982
  • Rauch A. et al. 2012. Lancet. 380: 1674-82. PubMed ID: 23020937
  • Risheg H. et al. 2007. Nature Genetics. 39: 451-3. PubMed ID: 17334363
  • Shaheen R. et al. 2013. American journal of human genetics. 92: 598-604. PubMed ID: 23522784
  • Shigemizu D. et al. 2015. Plos One. 10: e0130329. PubMed ID: 26132555
  • Southgate L. et al. 2011. American Journal of Human Genetics. 88: 574-85. PubMed ID: 21565291
  • Southgate L. et al. 2015. Circulation. Cardiovascular Genetics. 8: 572-581. PubMed ID: 25963545
  • Stef M. et al. 2007. European Journal of Human Genetics. 15: 843-7. PubMed ID: 17473832
  • Stevens C.A. 2014. Rubinstein-Taybi Syndrome. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJ, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301699
  • Stittrich A.B. et al. 2014. American Journal of Human Genetics. 95: 275-84. PubMed ID: 25132448
  • Tunovic S. et al. 2014. American Journal of Medical Genetics Part A. 164: 1744-9. PubMed ID: 24838796
  • Vergano S.S. et al. 2016. Coffin-Siris Syndrome. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 23556151
  • Wang T. et al. 2016. Nature Communications. 7: 13316. PubMed ID: 27824329
  • Wincent J. et al. 2009. European Journal of Medical Genetics. 52: 271-2. PubMed ID: 19248844
  • Yuan B. et al. 2015. The Journal of Clinical Investigation. 125: 636-51. PubMed ID: 25574841
Order Kits
TEST METHODS

NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most cases, we are unable to determine the phase of sequence variants.  In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants due to somatic mosaicism is limited.  Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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