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Xeroderma Pigmentosum Sequencing Panel

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

Sequencing

Test Code TestCPT Code Copy CPT Codes
1341 DDB2 81479 Add to Order
ERCC2 81479
ERCC3 81479
ERCC4 81479
ERCC5 81479
POLH 81479
XPA 81479
XPC 81479
Full Panel Price* $1890.00
Test Code Test Total Price CPT Codes Copy CPT Codes
1341 Genes x (8) $1890.00 81479(x8) Add to Order
Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information. If you would like to order a subset of these genes contact us to discuss pricing.

For Sanger Sequencing click here.
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

DNA testing confirms diagnosis in ~77% of XP patients. The proportion of XP patients that have mutations in XPA, XPC, ERCC2, ERCC4, and ERCC5 are 25%, 25%, 15%, 6%, and 6%, respectively. Individuals with XP variant will have mutations in POLH in 21% of cases. Causative mutations in the XPA gene are more common in Japan and rare in the United States and Europe. Causative mutations in the ERCC3 and DDB2 genes are rare (Kraemer and DiGiovanna 2013). Some individuals have a phenotype with both features of XP and Cockayne syndrome (i.e. increased skin cancer in XP and dysmyelination in CS). These XP/CS individuals have mutations in either the ERCC2, ERCC3 or ERCC5 genes (Rapin et al. 2000).

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Deletion/Duplication Testing via aCGH

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
600 DDB2$690.00 81479 Add to Order
ERCC2$690.00 81479
ERCC3$690.00 81479
ERCC4$690.00 81479
ERCC5$690.00 81479
POLH$690.00 81479
XPA$690.00 81479
XPC$690.00 81479
Full Panel Price* $840.00
Test Code Test Total Price CPT Codes Copy CPT Codes
600 Genes x (8) $840.00 81479(x8) 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

Copy number variations are a rare form of pathogenic variation among the genes in this test panel. Therefore, clinical sensitivity is predicted to be low.

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Clinical Features

Xeroderma pigmentosum (XP) results in skin changes (e.g. blistering due to sunburn (60% of cases), persistent erythema, freckling, and hyper/hypopigmentation), early onset skin cancers and internal cancers, ocular problems (e.g. severe keratitis, eyelid atrophy, and conjunctival inflammatory masses), and neurologic abnormalities (e.g. microcephaly, diminished/absent deep tendon stretch reflexes, progressive sensorineural hearing loss, and cognitive impairment) (Kraemer and DiGiovanna 2013). The types of cancers involved are usually non-melanoma skin cancers (basal and squamous cell) and cutaneous melanoma. The incidence of skin cancer is 1000 times the rate of the general population (Webb 2008). Sun exposure must be limited because skin cancer can appear within the first decade of life due to ultraviolet radiation; removal of early pre-cancerous lesions is beneficial. XP occurs in approximately 1 in 250,000 live births in the United States, 2.3 in 1,000,000 live births in Western Europe (Kleijer et al. 2008), and a higher prevalence of 1 in 22,000 live births in Japan (Hirai et al. 2006). Higher prevalence is also seen in North Africa, and the Middle East, possibly due to consanguinity. XP presents with complete penetrance, but shows a wide variety of clinical heterogeneity within and between XP groups. Heterogeneity may be due to length of sunlight exposure, complementation group, nature of mutation and unknown factors (Lehmann et al. 2011).

Genetics

Xeroderma pigmentosum is an autosomal recessive disorder caused by mutations in the XPA, ERCC3, XPC, ERCC2, DDB2, ERCC4, and ERCC5 genes, which belong to the XPA, XPB, XPC, XPD, XPE, XPF, and XPG complementation groups, respectively. The products of these genes are involved in DNA repair, specifically nucleotide excision repair (NER). This mechanism of repair involves removal of UV-induced dipyrimidine photoproducts and chemical crosslinks. If the damage is left unchecked, cells have the potential for cancer development. Specific genotype-phenotype correlations exist for the XP forms (Kraemer and DiGiovanna 2013). The XP variant phenotype, which is caused by POLH mutations leads to affected individuals who have an increased skin cancer incidence and eye abnormalities like most XP patients. Mutations in the POLH gene do not cause aberrant nucleotide excision repair, but have difficulty replicating DNA containing ultraviolet-induced damage (Lehmann et al. 2011).

The XPC and DDB2 (XPE) protein products are required for initial damage detection. Afterwards the products XPB and XPD open up DNA around the photoproduct. XPA verifies correct protein assembly and then the XPG and XPF nucleases cleave the DNA on either side of the damage for correct repair via the DNA polymerase η (encoded by POLH) (Naegeli and Sugasawa 2011; Kraemer and DiGiovanna 2013). Two types of NER are performed within the cell, namely, global genome repair and transcription coupled repair. The former is involved in global genome maintenance, whereas the latter is involved in repair of DNA from transcriptionally active genes. All aforementioned protein products are involved in transcription-coupled repair and most of these gene products are also involved with global genome repair, with the exception of XPC and XPE. Interestingly, patients with XPC or XPE mutations do not have severe sunlight lesions and neurological abnormalities, and this may have to do with their type of NER pathway involvement.

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

Testing Strategy

For this Next Generation (NextGen) panel, the full coding regions plus ~20 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 kit, 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, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Indications for Test

Individuals with a clinical presentation of XP. People with a family history of XP wanting to know their XP mutation status can also be tested. Carriers are asymptomatic, but the possibility of increased cancer risk is currently being assessed. Earlier diagnosis may improve patient prognosis through regular screening and treatment for early-onset malignancies. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

Genes

Official Gene Symbol OMIM ID
DDB2 600811
ERCC2 126340
ERCC3 133510
ERCC4 133520
ERCC5 133530
POLH 603968
XPA 611153
XPC 613208
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Xeroderma Pigmentosum via the DDB2 Gene
Xeroderma Pigmentosum via the ERCC2 Gene
Xeroderma Pigmentosum via the ERCC3 Gene
Xeroderma Pigmentosum via the ERCC4 Gene
Xeroderma Pigmentosum via the ERCC5 Gene
Xeroderma Pigmentosum via the POLH Gene
Xeroderma Pigmentosum via the XPA Gene
Xeroderma Pigmentosum via the XPC Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Hirai Y, Kodama Y, Moriwaki S-I, Noda A, Cullings HM, MacPhee DG, Kodama K, Mabuchi K, Kraemer KH, Land CE, Nakamura N. 2006. Heterozygous individuals bearing a founder mutation in the XPA DNA repair gene comprise nearly 1% of the Japanese population. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 601: 171–178. PubMed ID: 16905156
  • Kleijer WJ, Laugel V, Berneburg M, Nardo T, Fawcett H, Gratchev A, Jaspers NGJ, Sarasin A, Stefanini M, Lehmann AR. 2008. Incidence of DNA repair deficiency disorders in western Europe: Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. DNA Repair 7: 744–750. PubMed ID: 18329345
  • Kraemer KH, DiGiovanna JJ. 2013. Xeroderma Pigmentosum. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301571
  • Lehmann AR, McGibbon D, Stefanini M. 2011. Xeroderma pigmentosum. Orphanet J Rare Dis 6: 5. PubMed ID: 22044607
  • Naegeli H, Sugasawa K. 2011. The xeroderma pigmentosum pathway: Decision tree analysis of DNA quality. DNA Repair 10: 673–683. PubMed ID: 21684221
  • Rapin I, Lindenbaum Y, Dickson DW, Kraemer KH, Robbins JH. 2000. Cockayne syndrome and xeroderma pigmentosum. Neurology 55: 1442–1449. PubMed ID: 11185579
  • Webb S. 2008. Xeroderma pigmentosum. BMJ 336: 444–446. PubMed ID: 18292171
Order Kits
TEST METHODS

NextGen Sequencing

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
  • The first four pages of the requisition form must accompany all specimens.
  • Billing information is on the third and fourth pages.
  • Specimen and shipping instructions are listed on the fifth and sixth pages.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3-5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10-20 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 good for up to 48 hours.
  • If refrigerated, blood specimen is good for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • NextGen Sequencing Tests: Send in screw cap tube at least 10 µg of purified DNA at a concentration of at least 50 µg/ml
  • Sanger Sequencing Tests: Send in a screw cap tube at least 15 µg of purified DNA at a concentration of at least 20 µg/ml. For tests involving the sequencing of more than three genes, send an additional 5 µg DNA per gene. DNA may be shipped at room temperature.
  • Deletion/Duplication via aCGH: Send in screw cap tube at least 1 µg of purified DNA at a concentration of at least 100 µg/ml.
  • Whole-Genome Chromosomal Microarray: Collect at least 5 µg of DNA in TE (10 mM Tris-cl pH 8.0, 1mM EDTA), dissolved in 200 µl at a concentration of at least 100 ng/ul (indicate concentration on tube label). DNA extracted using a column-based method (Qiagen) or bead-based technology is preferred.

CELL CULTURE

(Delivery accepted Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Ship at least two T25 flasks of confluent cells.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We do not culture cells.