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Bleeding Disorders Sequencing Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
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TEST METHODS

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
1375 ABCG5 81479 Add to Order
ABCG8 81479
ACTN1 81479
ADAMTS13 81479
ANKRD26 81479
ANO6 81479
AP3B1 81479
BLOC1S3 81479
CD36 81479
CYCS 81479
DTNBP1 81479
F10 81479
F11 81479
F12 81479
F13A1 81479
F13B 81479
F2 81479
F5 81479
F7 81479
F8 81407
F9 81405
FGA 81479
FGB 81479
FGG 81479
FLI1 81479
FLNA 81479
GATA1 81479
GFI1B 81479
GGCX 81479
GP1BA 81479
GP1BB 81404
GP6 81479
GP9 81479
HOXA11 81479
HPS1 81479
HPS3 81479
HPS4 81479
HPS5 81479
HPS6 81479
ITGA2 81479
ITGA2B 81479
ITGB3 81479
LMAN1 81479
MASTL 81479
MCFD2 81479
MPL 81479
MYH9 81479
NBEAL2 81479
P2RX1 81479
P2RY12 81479
PLAU 81479
PRKACG 81479
RUNX1 81479
SERPINE1 81479
SERPINF2 81479
TBXA2R 81479
TBXAS1 81479
TUBB1 81479
VKORC1 81479
VWF 81408
WAS 81406
Full Panel Price* $2490.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1375 Genes x (61) $2490.00 81404, 81405, 81406, 81407, 81408, 81479(x56) 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

This test is designed to identify variants in genes associated with a variety of bleeding phenotypes. In a recent study of patients with excessive bleeding, a next generation sequencing approach was used for differential diagnosis. Of the 61 patients with a suspected etiology, a corresponding pathogenic variant was identified in 91.8% of cases. In 76 patients with an unknown etiology, a causative pathogenic variant was identified in 10.5% of cases (Simeoni et al. 2016).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 ADAMTS13$690.00 81479 Add to Order
ANKRD26$690.00 81479
ANO6$690.00 81479
AP3B1$690.00 81479
BLOC1S3$690.00 81479
CD36$690.00 81479
DTNBP1$690.00 81479
F10$690.00 81479
F11$690.00 81479
F12$690.00 81479
F13A1$690.00 81479
F13B$690.00 81479
F2$690.00 81479
F5$690.00 81479
F7$690.00 81479
F8$690.00 81406
F9$690.00 81479
FGA$690.00 81479
FGB$690.00 81479
FGG$690.00 81479
FLNA$690.00 81479
GATA1$690.00 81479
GGCX$690.00 81479
GP1BA$690.00 81479
GP1BB$690.00 81479
GP6$690.00 81479
GP9$690.00 81479
HPS1$690.00 81479
HPS3$690.00 81479
HPS4$690.00 81479
HPS5$690.00 81479
HPS6$690.00 81479
ITGA2$690.00 81479
ITGA2B$690.00 81479
ITGB3$690.00 81479
LMAN1$690.00 81479
MASTL$690.00 81479
MCFD2$690.00 81479
MPL$690.00 81479
MYH9$690.00 81479
NBEAL2$690.00 81479
P2RX1$690.00 81479
P2RY12$690.00 81479
PLAU$690.00 81479
RUNX1$690.00 81479
SERPINE1$690.00 81479
SERPINF2$690.00 81479
TBXA2R$690.00 81479
TBXAS1$690.00 81479
VKORC1$690.00 81479
VWF$690.00 81479
WAS$690.00 81479
Full Panel Price* $1670.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (52) $1670.00 81406, 81479(x51) 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

Large deletions in various inherited platelet disorders represent ~20% of causative variants found within AP3B1 and HPS3, ~10% in HPS6 and GP1BB, 2% in GP1BA, 5% in ITGA2B, 2% in ITGB3, and 100% in PLAU (Human Gene Mutation Database).

For coagulation deficiency genes, large deletions are represent 5% of causative variants in the F10, 2% in F11, 3% in F13A1, 2% in F5, 2% in F7, 6% in F8, 3% in F9, 15% in FGA, and 5% in VWF (Human Gene Mutation Database).

The majority of variants reported in the thrombocytopenia genes in this panel are missense and nonsense variants. Large deletions account for ~24% of the reported RUNX1 gene variants, but in general, large, multi-exon and whole gene deletions are rare among the thrombocytopenia panel genes. In addition to the RUNX1 gene, large deletions have also been reported in the GP1BB, MYH9, and WAS genes (Human Gene Mutation Database).

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Clinical Features

This sequencing panel focuses on inherited bleeding disorders due to impaired platelet function, coagulation factor deficiencies or thrombocytopenia. With many factors contributing to clot formation, differential diagnosis of the various bleeding disorders can be time-intensive, labor-intensive, and difficult to interpret, especially in patients with milder symptoms. Genetic testing provides a means to examine multiple bleeding disorder genes simultaneously to quickly identify potential causes to disease. Differential diagnosis is especially helpful in employing appropriate therapies to mitigate bleeding episodes (Westbury et al. 2015; Simeoni et al. 2016; Lentaigne et al. 2016).

Platelet function disorders (PFDs) tested in this panel include defects in platelet adhesion/coagulation, receptor function, or secretion (Handin et al 2005). PFDs due to defects in platelet adhesion include Bernard-Soulier syndrome and Scott Syndrome; defects in receptor function include Glanzmann’s thrombasthenia, Thromboxane A2 receptor deficiency, GPVI collagen receptor deficiency, and P2Y12 ADP receptor deficiency. Defects in storage granules include Hermansky-Pudlak Syndrome.

Coagulation factor deficiency panel includes testing for a large group of inherited bleeding disorders including three types of hemophilia, von Willebrand disease and rare bleeding disorders (RBD). RBDs include inherited deficiencies in fibrinogen, factor (F) II, FV, FV +FVIII, FVII, FX, FXI, FXIII, plasminogen activator inhibitor, and alpha-s-plasmin inhibitor.

Inherited thrombocytopenias comprise a heterogeneous group of rare disorders characterized by low platelet counts. In adults, low platelet numbers are typically considered below 150,000/microL. Bleeding manifestations of thrombocytopenia include primarily excessive bruising (purpura), petechiae, prolonged bleeding from cuts or from surgical procedures, spontaneous nose bleeds, and in women, heavy menstrual flows. Thrombocytopenia and consequent bleeding diatheses range in severity from mild to severe. About half of the inherited thrombocytopenias are syndromic disorders characterized by physical and neurological anomalies, and immunodeficiencies (Balduini et al. 2013). Some inherited thrombocytopenias are associated with an increased risk of developing myelodysplastic syndrome (MDS) and acute leukemia (AL) (Churpek et al. 2013). It is important to distinguish inherited thrombocytopenias from immune / idiopathic thrombocytopenias (ITP) in order to inform clinical management and identify potential at risk family members.

Genetics

Inherited platelet function disorders are inherited in an autosomal recessive manner due to pathogenic variants in the ITGB3, ITGA2B, AP3B1, BLOCK1S3, DTNBP1, HPS1, HPS3, HPS4, HPS5, HPS6, ANO6, GP1BA, GP9, GP1BB, P2RY12, CD36 and GP6 genes (Handin et al. 2005; Watson et al. 2013). Autosomal dominant forms include pathogenic variants in the TBXA2R, PLAU, PTGS1, and TBXAS1 genes.

Hemophilia A and B are inherited through an X-linked recessive manner through pathogenic variants in the F8 and F9 genes respectively and primarily affect males. VWD is inherited in both autosomal dominant and recessive manners through pathogenic variants in the VWF gene. RBDs are all inherited in an autosomal recessive manner with deficiencies in FVII, FXI, or FV accounting for ~80% of cases. RBD genes include FGA, FGB, FGG, F2, F5, F7, F10, F11, F12, F13A1, F13B, MCFD2, LMAN1, SERPINE1, SERPINF2, VKORC1, and GGCX. See individual test descriptions for additional information on the molecular biology of each gene.

Thrombocytopenia genes included in this panel have been associated with both syndromic and non-syndromic forms of inherited thrombocytopenia and represent the most well-documented forms of inherited thrombocytopenia reported in the literature. Thrombocytopenias are typically divided into three distinct groups based upon platelet size: large / macrothrombocytopenias, small / microthrombocytopenias, and thrombocytopenias with normal sized platelets (Westbury et al. 2015; Simeoni et al. 2016; Lentaigne et al. 2016).

Testing Strategy

For this NGS test, the full coding regions plus ~20bp 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 detect inversions in the F8 gene which account for about 40% of Hemophilia A cases.

This panel provides 100% coverage of the aforementioned regions of the indicated genes. We define coverage as > 20X NGS reads for exons 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 testing include patients with excessive bleeding of unknown etiology due to abnormal platelet count, volume, morphology, function, or impaired coagulation. This test especially aids in a rapid differential diagnosis of phenotypically similar disorders, rules out particular syndromes, and provides the analysis of multiple genes simultaneously. Individuals who are suspected of any of these disorders, especially if clinical diagnosis is unclear and individuals who have been found to be negative by mutation analysis for a single gene test are candidates (Othman 2013; Peyvandi et al. 2012).

Diseases

Name Inheritance OMIM ID
Afibrinogenemia, congenital AR 202400
Anti-Plasmin Deficiency, Congenital AR 262850
Bernard Soulier Syndrome AR 231200
Bleeding Disorder, Platelet-Type, 11 AR 614201
Bleeding Disorder, Platelet-Type, 13, Susceptibility To AD 614009
Bleeding Disorder, Platelet-Type, 14 AD 614158
Bleeding Disorder, Platelet-Type, 15 AD 615193
Bleeding Disorder, Platelet-Type, 17 AD 187900
Bleeding Disorder, Platelet-Type, 19 AR 616176
Bleeding Disorder, Platelet-Type, 8 AR 609821
Bleeding Disorder, Platelet-Type, 9 AD 614200
Cardiac Valvular Dysplasia, X-Linked XL 314400
Congenital Amegakaryocytic Thrombocytopenia AR 604498
Factor V And Factor VIII, Combined Deficiency Of, 1 AR 227300
Factor V And Factor VIII, Combined Deficiency Of, 2 AR 613625
Factor V Deficiency AR 227400
Factor VII Deficiency AR 227500
Factor X Deficiency AR 227600
Factor XII Deficiency Disease AR 234000
Factor XIII, A Subunit, Deficiency Of AR 613225
Factor XIII, B Subunit, Deficiency Of AR 613235
GATA-1-Related Thrombocytopenia With Dyserythropoiesis XL 300367
Glanzmann's Thrombasthenia AR 273800
Gray Platelet Syndrome AR 139090
Hemophilia A, Congenital XL 134500
Hereditary Factor IX Deficiency Disease AD,AR 306900
Hereditary Factor XI Deficiency Disease AR 612416
Hermansky Pudlak Syndrome 2 AR 608233
Hermansky-Pudlak Syndrome 1 AR 203300
Hermansky-Pudlak Syndrome 3 AR 614072
Hermansky-Pudlak Syndrome 4 AR 614073
Hermansky-Pudlak Syndrome 5 AR 614074
Hermansky-Pudlak Syndrome 6 AR 614075
Hermansky-Pudlak Syndrome 7 AR 614076
Hermansky-Pudlak Syndrome 8 AD 614077
Macrothrombocytopenia, Autosomal Dominant, TUBB1-Related AD 613112
May-Hegglin Anomaly AR 155100
Plasminogen Activator Inhibitor Type 1 Deficiency AR 613329
Platelet Glycoprotein IV Deficiency AR 608404
Prothrombin Deficiency, Congenital AR 613679
Pseudoxanthoma Elasticum-Like Disorder With Multiple Coagulation Factor Deficiency AD 610842
Quebec Platelet Disorder AD 601709
Radioulnar Synostosis With Amegakaryocytic Thrombocytopenia AR 605432
Scott Syndrome AR 262890
Sitosterolemia AD 210250
Thrombocytopenia 2 AD 188000
Thrombocytopenia 4 AD 612004
Thrombocytopenia, Familial, With Propensity To Acute Myelogenous Leukemia AD 601399
Thrombocytopenia, Paris-Trousseau Type AR 188025
Thrombotic Thrombocytopenic Purpura AR 274150
Vitamin K-Dependent Clotting Factors, Combined Deficiency Of, 2 AD 607473
Von Willebrand Disease, Type 1 XL 193400

Related Tests

Name
MYH9-Related Disorders via the MYH9 Gene
ADP Receptor Deficiency via the P2RY12 Gene
Anti-Plasmin Deficiency via the SERPINF2 Gene
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Bernard-Soulier Syndrome via the GP1BA Gene
Bernard-Soulier Syndrome via the GP1BB Gene
Bernard-Soulier Syndrome via the GP9 Gene
Coagulation Factor Deficiency Sequencing Panel
Combined Factor V and Factor VIII Deficiency via the LMAN1 Gene
Combined Factor V and Factor VIII Deficiency via the MCFD2 Gene
Comprehensive Cardiology Sequencing Panel with CNV Detection
Congenital Abnormalities of the Kidney and Urinary Tract (CAKUT) Sequencing Panel with CNV Detection
Congenital Amegakaryocytic Thrombocytopenia (CAMT) and Thrombocythemia 2 via the MPL Gene
Congenital Dyserythropoietic Anemia Sequencing Panel
Congenital Factor XIII deficiency via the F13A1 Gene
Congenital Factor XIII Deficiency via the F13B Gene
Congenital Fibrinogen Deficiency Sequencing Panel
Congenital Fibrinogen Deficiency via the FGA Gene
Congenital Fibrinogen Deficiency via the FGB Gene
Congenital Fibrinogen Deficiency via the FGG Gene
Factor V Deficiency via the F5 Gene
Factor VII Deficiency via the F7 Gene
Factor X Deficiency via the F10 Gene
Familial Platelet Function Disorder via the GP6 Gene
Glanzmann's Thrombasthenia Sequencing Panel
Glanzmann's Thrombasthenia via the ITGA2B Gene
Glanzmann's Thrombasthenia via the ITGB3 Gene
Gray Platelet Syndrome via the NBEAL2 Gene
Hemophilia A via the F8 Gene
Hemophilia B via the F9 Gene
Hemophilia C via the F11 Gene
Hermansky-Pudlak Syndrome (HPS) Sequencing Panel
Hermansky-Pudlak Syndrome Type 1 (HPS1) via the HPS1 Gene
Hermansky-Pudlak Syndrome Type 2 (HPS2) via the AP3B1 Gene
Hermansky-Pudlak Syndrome Type 3 (HPS3) via the HPS3 Gene
Hermansky-Pudlak Syndrome Type 4 (HPS4) via the HPS4 Gene
Hermansky-Pudlak Syndrome Type 5 (HPS5) via the HPS5 Gene
Hermansky-Pudlak Syndrome Type 6 (HPS6) via the HPS6 Gene
Hermansky-Pudlak Syndrome Type 7 (HPS7) via the DTNBP1 Gene
Hermansky-Pudlak Syndrome Type 8 (HPS8) via the BLOC1S3 Gene
Hermansky-Pudlak Syndrome via the HPS3 Gene, Exon 1 Deletion
Marfan Syndrome and Related Aortopathies Sequencing Panel
Nonsyndromic Hearing Loss and Deafness Sequencing Panel
Oculocutaneous Albinism Sequencing Panel
Otopalatodigital Spectrum Disorders, Periventricular Nodular Heterotopia and Cardiac Valvular Dystrophy via the FLNA Gene
Paris-Trousseau Thrombocytopenia via the FLI1 Gene
Platelet Function Disorder Sequencing Panel
Prothrombin/Factor II Deficiency via the F2 Gene
Scott Syndrome via the ANO6 Gene
Severe Congenital Neutropenia Sequencing Panel
Sitosterolemia Sequencing Panel
Sitosterolemia via the ABCG5 Gene
Sitosterolemia via the ABCG8 Gene
Thrombocytopenia and Predisposition to Myeloid Malignancies via the ANKRD26 Gene
Thrombocytopenia Sequencing Panel
Thrombocytopenia Sequencing Panel - Expanded
Thrombocytopenia via the CYCS Gene
Thrombocytopenia via the GATA1 Gene
Thrombocytopenia via the MASTL Gene
Thrombocytopenia with Predisposition to Acute Myelogenous Leukemia via the RUNX1 Gene
Thrombotic Thrombocytopenic Purpura (TTP) via the ADAMTS13 Gene
Thromboxane A2 Receptor Deficiency via the TBXA2R Gene
von Willebrand Disease Types 1, 2, and 3 via the VWF Gene
Wiskott-Aldrich Syndrome, X-linked Thrombocytopenia, and X-linked Congenital Neutropenia, via the WAS Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Balduini C.L. et al. 2013. Journal of Thrombosis and Haemostasis. 11: 1006-19. PubMed ID: 23510089
  • Churpek J.E. et al. 2013. Leukemia & Lymphoma. 54: 28-35. PubMed ID: 22691122
  • Handin R.I. 2005. Hematology. American Society of Hematology Education Program. 396-402. PubMed ID: 16304410
  • Human Gene Mutation Database (Bio-base).
  • Klopocki E. et al. 2006. European Journal of Human Genetics. 14: 1274-9. PubMed ID: 16896345
  • Lentaigne C. et al. 2016. Blood. 127: 2814-23. PubMed ID: 27095789
  • Othman M. 2013. Seminars in Thrombosis and Hemostasis. 39: 575-8. PubMed ID: 23982907
  • Papoulidis .I et al. 2014. Molecular Medicine Reports. 9: 163-5. PubMed ID: 24220582
  • Peyvandi F. et al. 2012. Haemophilia. 18 Suppl 4: 148-53. PubMed ID: 22726099
  • Simeoni I. et al. 2016. Blood. 127: 2791-803. PubMed ID: 27084890
  • Watson S.P. et al. 2013. Journal of Thrombosis and Haemostasis. 11 Suppl 1: 351-63. PubMed ID: 23516995
  • Westbury S.K. et al. 2015. Genome Medicine. 7: 36. PubMed ID: 25949529
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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