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Cholestasis Sequencing Panel
- Summary and Pricing
- Clinical Features and Genetics
- Citations
- Methods
- Ordering/Specimens
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TEST METHODS
- NextGen Sequencing using PG-Select Capture Probes
- Deletion/Duplication Testing via Array Comparative Genomic Hybridization
NextGen Sequencing
| Test Code | Test Copy Genes | CPT Code Copy CPT Codes | |
|---|---|---|---|
| 1963 | ABCB11 | 81479 | Add |
| ABCB4 | 81479 | ||
| AKR1D1 | 81479 | ||
| ATP8B1 | 81479 | ||
| BAAT | 81479 | ||
| CLDN1 | 81479 | ||
| HSD3B7 | 81479 | ||
| JAG1 | 81407 | ||
| NOTCH2 | 81479 | ||
| NR1H4 | 81479 | ||
| SERPINA1 | 81479 | ||
| SLC25A13 | 81479 | ||
| TJP2 | 81479 | ||
| VIPAS39 | 81479 | ||
| VPS33B | 81479 | ||
| Full Panel Price* | $640.00 | ||
| Test Code | Test Copy Genes | Total Price | CPT Codes Copy CPT Codes | |
|---|---|---|---|---|
| 1963 | Genes x (15) |
$640.00 | 81407, 81479(x14) | Add |
Pricing Comments
We are happy to accommodate requests for single genes or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered on our PGxome Custom Panel.
Targeted Testing
For ordering sequencing of targeted known variants, please proceed to our Targeted Variants landing page.
Turnaround Time
The great majority of tests are completed within 20 days.
Clinical Sensitivity
Detection rate of pathogenic variants in each gene of this panel in a large cohort of patients with cholestasis of undefined etiology is unknown. In a study of 51 subjects with cholestasis of undefined etiology, Matte et al. found causative variants in JAG1, ATP8B1, ABCB11, or ABCB4 genes in 14 patients (27%) (Matte et al. 2010). ATP8B1 and ABCB11 causative variants were found in 12 (21%) and 36 (63%) respectively of 57 families affected by PFIC with normal GGT activity (Davit-Spraul et al. 2010). In a cohort study of 68 unrelated PFIC3 patients, ABCB4 causative variants were found at both alleles in 13 patients (19%) and only one allele in 5 patients (7%), respectively (Degiorgio et al. 2007). Out of 29 families that had chronic cholestatic liver disease with low GGT and did not have causative variants in ABCB11 or ATP8B1, TJP2 mutations were found in 8 families (27.6%) (Sambrotta et al. 2014).
Del/Dup via aCGH
| Test Code | Test Copy Genes | Price | CPT Code Copy CPT Codes | |
|---|---|---|---|---|
| 600 | ABCB11 | $990.00 | 81479 | Add |
| ABCB4 | $990.00 | 81479 | ||
| AKR1D1 | $990.00 | 81479 | ||
| ATP8B1 | $990.00 | 81479 | ||
| BAAT | $990.00 | 81479 | ||
| CLDN1 | $990.00 | 81479 | ||
| HSD3B7 | $990.00 | 81479 | ||
| JAG1 | $990.00 | 81406 | ||
| NOTCH2 | $990.00 | 81479 | ||
| NR1H4 | $990.00 | 81479 | ||
| SERPINA1 | $990.00 | 81479 | ||
| SLC25A13 | $990.00 | 81479 | ||
| TJP2 | $990.00 | 81479 | ||
| VIPAS39 | $990.00 | 81479 | ||
| VPS33B | $990.00 | 81479 | ||
| Full Panel Price* | $1490.00 | |||
| Test Code | Test Copy Genes | Total Price | CPT Codes Copy CPT Codes | |
|---|---|---|---|---|
| 600 | Genes x (15) |
$1490.00 | 81406, 81479(x14) | Add |
Pricing Comments
|
# of Genes Ordered |
Total Price |
|
1 |
$990 |
|
2-5 |
$1190 |
|
6-10 |
$1290 |
|
11-100 |
$1490 |
|
Over 100 |
Call for quote |
Turnaround Time
The great majority of tests are completed within 20 days.
Clinical Sensitivity
The prevalence of large deletions (vast majority) and duplications affecting the JAG1 gene are expected to be about 5% in Alagille syndrome (Warthen et al. 2006). To date, only two large deletions have been found to affect the VPS33B gene, accounting for 4% of total documented pathogenic variants in this gene (Human Gene Mutation Database). No gross deletions or duplications have been reported in VIPAS39. Large deletions and duplications (more often) have been found in the SLC25A13 locus, accounting for 7% of all documented pathogenic variants in this gene (Human Gene Mutation Database). In a study of 68 East Asian patients affected by citrin deficiency (CD), one patient (1.5%) was found to have a large SLC25A13 duplication (Song et al. 2013).
Clinical Features
Cholestasis is characterized by jaundice and pruritus. It can present as the hallmark feature in progressive familial intrahepatic cholestasis (PFIC) or as a feature in other inherited disorders such as Alagille syndrome.PFIC is a group of autosomal recessive liver disorders due to defects in bile secretion and is characterized by intrahepatic cholestasis with disease onset usually in infancy and childhood (Srivastava 2014; Davit-Spraul et al. 2009). Four types of PFIC have been classified in terms of causative genes involved in the hepatocellular transport system. FIC1 (familial intrahepatic cholestasis protein 1 deficiency (PFIC1) is caused by mutations in ATP8B1, and BSEP (bile salt export pump). PFIC2 is caused by mutations in ABCB11. PFIC3 is caused by reduced biliary phospholipid secretion due to mutations in ABCB4. The most recently identified PFIC4 is caused by abnormal tight junctions between adjacent hepatocytes and biliary canaliculi in liver tissue due to TJP2 defects (Sambrotta et al. 2014). PFIC patients usually develop fibrosis and end-stage liver disease before adulthood. Serum gamma-glutamyl transferase (GGT) activity is normal in PFIC1 and PFIC2 patients, elevated in PFIC3 patients and low in PFIC4 patients.Defects in PFIC-associated genes ATP8B1 and ABCB11 can also cause a milder type of liver disease called benign recurrent intrahepatic cholestasis (BRIC) (Klomp et al. 2004; Beauséjour et al. 2011). BRIC is an autosomal recessive disorder characterized by intermittent episodes of cholestasis without progression to liver failure.Other inherited disorders featuring cholestasis includes Alagille syndrome (JAG1 and NOTCH2), arthrogryposis, renal dysfunction, and cholestasis syndrome (ARC syndrome; VPS33B and VIPAS39), alpha-1-antitrypsin deficiency (SERPINA1), citrullinemia (SLC25A13), congenital defects of bile acid synthesis (HSD3B7 and AKR1D1), familial hypercholanemia (TJP2 and BAAT) and neonatal ichthyosis-sclerosing cholangitis syndrome (CLDN1). More information about each gene can be found in the Genetics section below.
Genetics
Progressive familial intrahepatic cholestasis (PFIC) is inherited in an autosomal recessive manner. Defects in four genes to date encoding proteins associated with hepatocellular transport system have been found to cause PFIC: ATP8B1, ABCB11, ABCB4 and TJP2 (Srivastava et al. 2014; Davit-Spraul et al. 2009; Sambrotta et al. 2014) (see also Clinical Features above). The ATP8B1 gene (27 coding exons) encodes the FIC1 protein, which is a member of the P-type cation transport ATPase family. Pathogenic defects in ATP8B1 include missense, nonsense, splicing site mutations, small indels and exon-level large deletions (Human Gene Mutation Database). In addition to PFIC1, recessive ATP8B1 mutations can also cause benign recurrent intrahepatic cholestasis-1 (BRIC1). The ABCB11 (27 coding exons) gene encodes the bile salt export pump protein (BSEP), which is a member of the superfamily of ATP-binding cassette (ABC) transporters. Pathogenic defects in ABCB11 include missense, nonsense, splicing site mutations and small indels and exon-level large deletions (Human Gene Mutation Database). In addition to PFIC2, recessive ABCB11 mutations can also cause benign recurrent intrahepatic cholestasis-2 (BRIC2). The ABCB4 gene (27 coding exons) encodes the multi-drug resistant 3 protein (MDR3), which is also a member of the superfamily of ATP-binding cassette (ABC) transporters. Pathogenic defects in ABCB4 include missense, nonsense, splicing site mutations, small indels and exon-level large deletions (Human Gene Mutation Database). The newly found fourth PFIC gene TJP2 (23 coding exons) encodes the tight junction protein 2, which is involved in the organization of epithelial and endothelial intercellular junctions. Pathogenic defects in TJP2 include missense, nonsense, splicing site mutations, small indels and exon-level large deletions (Human Gene Mutation Database). TJP2 defects can also cause familial hypercholanemia, which is characterized by elevated serum bile acid concentrations, itching, and fat malabsorption (Carlton et al. 2003).
Genes associated with other inherited disorders featuring cholestasis are described as follows.The JAG1 gene (26 coding exons) encodes the ligand for the receptor Notch 1 in the Notch signaling pathway. Dominant JAG1 mutations cause Alagille syndrome (Oda et al. 1997; Warthen et al. 2006) (see Test # 427).The NOTCH2 gene (34 coding exons) encodes the receptor Notch 2 in the Notch signaling pathway. Dominant NOTCH2 mutations can cause both Alagille syndrome (McDaniell et al. 2006) and the skeletal disorder Hajdu-Cheney syndrome (Simpson et al. 2011).The VPS33B gene (23 coding exons) encodes a homolog of the yeast vacuolar sorting protein Vps33, which is a cytosolic protein involved in vesicle membrane fusion. Recessive VPS33B mutations are the major causes for arthrogryposis, renal dysfunction, and cholestasis syndrome (ARC syndrome) (Gissen et al. 2004) (see Test # 248).The VIPAS39 gene (21 coding exons) encodes the VPS33B interacting protein, apical-basolateral polarity regulator (VIPAR). Recessive VIPAS39 mutations are a less common cause for arthrogryposis, renal dysfunction, and cholestasis syndrome (ARC syndrome) (Cullinane et al. 2010) (see Test # 591).The SERPINA1 gene (4 coding exons) encodes alpha-1-antitrypsin (AAT), also known as protease inhibitor (PI), a major plasma serine protease inhibitor. Recessive SERPINA1 mutations cause alpha-1-antitrypsin deficiency (Medicina et al. 2009).The SLC25A13 gene (18 coding exons) encodes citrin, a calcium-dependent mitochondrial solute transporter with a role in urea cycle function. Recessive SLC25A13 mutations can cause both adult-onset type II citrullinemia (Kobayashi et al. 1999) and neonatal-onset type II citrullinemia (Tazawa et al. 2004).The HSD3B7 gene (7 coding exons) encodes 3 beta-hydroxysteroid dehydrogenase type 7, which is an enzyme in the production of bile acids. Recessive HSD3B7 mutations cause congenital bile acid synthesis defect type 1 (CBAS1) (Cheng et al. 2003).The AKR1D1 gene (9 coding exons) encodes the steroid 5-beta-reductase, which is responsible for catalysis of the 5-beta-reduction of bile acid intermediates and steroid hormones carrying a delta (4)-3-one structure. Recessive AKR1D1 mutations cause congenital bile acid synthesis defect type 2 (CBAS2) (Lemonde et al. 2003).The NR1H4 gene (9 coding exons) encodes a ligand-activated transcription factor, which functions as a receptor for bile acids. A heterozygous nonsense NR1H4 mutation has been reported in idiopathic infantile cholestasis (Chen et al. 2012).The BAAT gene (3 coding exons) encodes bile acid-CoA:amino acid N-acyltransferase, a liver enzyme that catalyzes the transfer of C24 bile acids from the acyl-CoA thioester to either glycine or taurine. Recessive BAAT mutations cause bile acid amidation defect (Setchell et al. 2013).The CLDN1 gene (4 coding exons) encodes a member of the claudin family, which is an integral membrane protein and a component of tight junction strands. Recessive CLDN1 mutations result in neonatal ichthyosis-sclerosing cholangitis syndrome (NISCH) (Feldmeyer et al. 2006).
Testing Strategy
This NextGen Sequencing Panel analyzes 16 genes that have been associated with cholestasis. For this NGS panel, the full coding regions, plus ~10 bp of non-coding DNA flanking each exon, are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization method, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, undocumented and questionable variant calls are confirmed by Sanger sequencing.
This test does not currently include sequencing or gene-centric aCGH for exons 1 to 4 of the NOTCH2 gene because of high sequence similarity to one or more additional chromosomal regions. So far, no pathogenic variants have been reported in these exons.
Indications for Test
Candidates for this test are patients with cholestasis. This test especially aids in a differential diagnosis of similar phenotypes by analyzing multiple genes simultaneously.
Genes
| Official Gene Symbol | OMIM ID |
|---|---|
| ABCB11 | 603201 |
| ABCB4 | 171060 |
| AKR1D1 | 604741 |
| ATP8B1 | 602397 |
| BAAT | 602938 |
| CLDN1 | 603718 |
| HSD3B7 | 607764 |
| JAG1 | 601920 |
| NOTCH2 | 600275 |
| NR1H4 | 603826 |
| SERPINA1 | 107400 |
| SLC25A13 | 603859 |
| TJP2 | 607709 |
| VIPAS39 | 613401 |
| VPS33B | 608552 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Diseases
Related Tests
CONTACTS
Genetic Counselors
- Genetic Counselor Team - clinicaldnatesting@preventiongenetics.com
Geneticist
- Wuyan Chen, PhD - wuyan.chen@preventiongenetics.com
Citations
- Beauséjour Y. et al. 2011. Canadian Journal of Gastroenterology = Journal Canadien De Gastroenterologie. 25: 311-4. PubMed ID: 21766090
- Carlton VEH, Harris BZ, Puffenberger EG, Batta AK, Knisely AS, Robinson DL, Strauss KA, Shneider BL, Lim WA, Salen G, Morton DH, Bull LN. 2003. Complex inheritance of familial hypercholanemia with associated mutations in TJP2 and BAAT. Nat. Genet. 34: 91–96. PubMed ID: 12704386
- Chen X-Q, Wang L-L, Shan Q-W, Tang Q, Deng Y-N, Lian S-J, Yun X. 2012. A novel heterozygous NR1H4 termination codon mutation in idiopathic infantile cholestasis. World J Pediatr 8: 67–71. PubMed ID: 21633855
- Cheng JB, Jacquemin E, Gerhardt M, Nazer H, Cresteil D, Heubi JE, Setchell KDR, Russell DW. 2003. Molecular genetics of 3beta-hydroxy-Delta5-C27-steroid oxidoreductase deficiency in 16 patients with loss of bile acid synthesis and liver disease. J. Clin. Endocrinol. Metab. 88: 1833–1841. PubMed ID: 12679481
- Cullinane AR, Straatman-Iwanowska A, Zaucker A, Wakabayashi Y, Bruce CK, Luo G, Rahman F, Gürakan F, Utine E, Ozkan TB, Denecke J, Vukovic J, Di Rocco M, Mandel H, Cangul H, Matthews RP, Thomas SG, Rappoport JZ, Arias IM, Wolburg H, Knisely AS, Kelly DA, Müller F, Maher ER, Gissen P. 2010. Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. Nat. Genet. 42: 303–312. PubMed ID: 20190753
- Davit-Spraul A. et al. 2009. Orphanet Journal of Rare Diseases. 4: 1. PubMed ID: 19133130
- Davit-Spraul A. et al. 2010. Hepatology (baltimore, Md.). 51: 1645-55. PubMed ID: 20232290
- Degiorgio D. et al. 2007. European Journal of Human Genetics : Ejhg. 15: 1230-8. PubMed ID: 17726488
- Feldmeyer L, Huber M, Fellmann F, Beckmann JS, Frenk E, Hohl D. 2006. Confirmation of the origin of NISCH syndrome. Hum. Mutat. 27: 408–410. PubMed ID: 16619213
- Gissen P, Johnson CA, Morgan NV, Stapelbroek JM, Forshew T, Cooper WN, McKiernan PJ, Klomp LWJ, Morris AAM, Wraith JE, McClean P, Lynch SA, Thompson RJ, Lo B, Quarrell OW, Di Rocco M, Trembath RC, Mandel H, Wali S, Karet FE, Knisely AS, Houwen RH, Kelly DA, Maher ER. 2004. Mutations in VPS33B, encoding a regulator of SNARE-dependent membrane fusion, cause arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome. Nat. Genet. 36: 400–404. PubMed ID: 15052268
- Human Gene Mutation Database (Bio-base).
- Klomp L.W. et al. 2004. Hepatology (baltimore, Md.). 40: 27-38. PubMed ID: 15239083
- Kobayashi K, Sinasac DS, Iijima M, Boright AP, Begum L, Lee JR, Yasuda T, Ikeda S, Hirano R, Terazono H, Crackower MA, Kondo I, Tsui LC, Scherer SW, Saheki T. 1999. The gene mutated in adult-onset type II citrullinaemia encodes a putative mitochondrial carrier protein. Nat. Genet. 22: 159–163. PubMed ID: 10369257
- Lemonde H.A. et al. 2003. Gut. 52: 1494-9. PubMed ID: 12970144
- Matte U. et al. 2010. Journal of Pediatric Gastroenterology and Nutrition. 51: 488-93. PubMed ID: 20683201
- McDaniell R, Warthen DM, Sanchez-Lara PA, Pai A, Krantz ID, Piccoli DA, Spinner NB. 2006. NOTCH2 mutations cause Alagille syndrome, a heterogeneous disorder of the notch signaling pathway. Am. J. Hum. Genet. 79: 169–173. PubMed ID: 16773578
- Medicina D, Montani N, Fra AM, Tiberio L, Corda L, Miranda E, Pezzini A, Bonetti F, Ingrassia R, Scabini R, Facchetti F, Schiaffonati L. 2009. Molecular characterization of the new defective P(brescia) alpha1-antitrypsin allele. Hum. Mutat. 30: E771–781. PubMed ID: 19437508
- Oda T, Elkahloun AG, Pike BL, Okajima K, Krantz ID, Genin A, Piccoli DA, Meltzer PS, Spinner NB, Collins FS, Chandrasekharappa SC. 1997. Mutations in the human Jagged1 gene are responsible for Alagille syndrome. Nat. Genet. 16: 235–242. PubMed ID: 9207787
- Sambrotta M. et al. 2014. Nature Genetics. 46: 326-8. PubMed ID: 24614073
- Setchell KDR, Heubi JE, Shah S, Lavine JE, Suskind D, Al–Edreesi M, Potter C, Russell DW, O’Connell NC, Wolfe B, Jha P, Zhang W, Bove KE, Knisely AS, Hofmann AF, Rosenthal P, Bull LN. 2013. Genetic Defects in Bile Acid Conjugation Cause Fat-Soluble Vitamin Deficiency. Gastroenterology 144: 945–955.e6. PubMed ID: 23415802
- Simpson MA, Irving MD, Asilmaz E, Gray MJ, Dafou D, Elmslie FV, Mansour S, Holder SE, Brain CE, Burton BK, Kim KH, Pauli RM, Aftimos S, Stewart H, Kim CA, Holder-Espinasse M, Robertson SP, Drake WM, Trembath RC. 2011. Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss. Nat. Genet. 43: 303–305. PubMed ID: 21378985
- Song Y-Z, Zhang Z-H, Lin W-X, Zhao X-J, Deng M, Ma Y-L, Guo L, Chen F-P, Long X-L, He X-L, Sunada Y, Soneda S, Nakatomi A, Dateki S, Ngu LH, Kobayashi K, Saheki T. 2013. SLC25A13 Gene Analysis in Citrin Deficiency: Sixteen Novel Mutations in East Asian Patients, and the Mutation Distribution in a Large Pediatric Cohort in China. PLoS ONE 8: e74544. PubMed ID: 24069319
- Srivastava A. 2014. Journal of Clinical and Experimental Hepatology. 4: 25-36. PubMed ID: 25755532
- Tazawa Y, Kobayashi K, Abukawa D, Nagata I, Maisawa S, Sumazaki R, Iizuka T, Hosoda Y, Okamoto M, Murakami J, Kaji S, Tabata A, Lu YB, Sakamoto O, Matsui A, Kanzaki S, Takada G, Saheki T, Iinuma K, Ohura T. 2004. Clinical heterogeneity of neonatal intrahepatic cholestasis caused by citrin deficiency: case reports from 16 patients. Mol. Genet. Metab. 83: 213–219. PubMed ID: 15542392
- Warthen DM, Moore EC, Kamath BM, Morrissette JJD, Sanchez-Lara PA, Sanchez P, Piccoli DA, Krantz ID, Spinner NB. 2006. Jagged1 (JAG1) mutations in Alagille syndrome: increasing the mutation detection rate. Hum. Mutat. 27: 436–443. PubMed ID: 16575836
Order Kits
TEST METHODS
- NextGen Sequencing using PG-Select Capture Probes
- Deletion/Duplication Testing via Array Comparative Genomic Hybridization
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 ~10 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 often covered 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 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 ~10 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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