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Facial Dysostosis Related 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
1973 CREBBP 81407 Add to Order
DHODH 81479
EFTUD2 81479
EP300 81479
FGFR1 81405
FGFR2 81479
FGFR3 81479
HDAC8 81479
NIPBL 81479
POLR1C 81479
POLR1D 81479
RAD21 81479
SF3B4 81479
SMC1A 81479
SMC3 81479
SRCAP 81479
TCF12 81479
TCOF1 81479
TWIST1 81404
Full Panel Price* $1690.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1973 Genes x (19) $1690.00 81404, 81405, 81407, 81479(x16) 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

Craniosynostosis and Related Disorders: ~61% (111/182) of 182 Spanish craniosynostosis probands harbor a pathogenic variant in one of the FGFR2, FGFR3, TWIST1 and TCF12 genes. Pathogenic variants in FGFR2, FGFR3, TWIST and TCF12 account for 36%, 16%, 8% and 3% of pathogenic variants identified in this study, respectively (Paumard-Hernández et al. 2014). TCF12 explains 32% and 10% of patients affected with bilateral and unilateral Craniosynostosis, respectively (Sharma et al. 2013). One study reported that six unique FGFR1 pathogenic missense variants were found in seven unrelated patients affected with Hartsfield syndrome (Simonis et al. 2013). FGFR1 explains 5% of Pfeiffer syndrome type 1 cases (Robin et al. 2011).

Treacher Collins syndrome, Mandibulofacial Dysostosis/, Miller syndrome and Acrofacial dysostosis, Nager type: TCOF1 pathogenic variants were found in ~70% of clinical diagnosed TCS cases, and large deletions are ~5% of reported TCOF1 pathogenic variants (Bowman et al. 2012; Katsanis and Jabs 2012). POLR1D pathogenic variants were identified in 20 out of 242 (8%) unrelated TCS patients who were negative for TCOF1 variants. To date, only one large deletion has been reported (Dauwerse et al. 2010). POLR1C pathogenic variants were identified in 3 out of 242 (~1%) unrelated patients with TCS or TCS phenotypic spectrum, who were negative for TCOF1 variants (Dauwerse et al. 2010). Sequencing may detect up to 85% of disease causing mutations in clinically diagnosed Mandibulofacial Dysostosis, Guion-Almeida Type cases. Large deletion/insertions involving EFTUD2 cause ~15% of cases, which cannot be identified by sequencing (Lines 2012; Gordon et al. 2012; Need et al. 2012; Human Gene Mutation Database). Rainger et al (2012) identified compound heterozygous pathogenic variants in DHODH in three out of eight unrelated families with Miller syndrome (Rainger et al. 2012). Bernier et al. (2012) identified 18 different heterozygous SF3B4 pathogenic variants in 20 (57%) of 35 families affected by Acrofacial dysostosis, Nager type. Analytical sensitivity should be high because almost all of the documented SF3B4 pathogenic variants are point mutations, and small deletion/insertions which are expected to be detected by direct sequencing of genomic DNA.

Rubinstein-Taybi syndrome and Floating-Harbor Syndrome: 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 (size 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). In one study, SRCAP pathogenic variants were found in 6 out of 9 patients with Floating-Harbor syndrome (Le Goff et al. 2013).

Cornelia de Lange Syndrome: Over 70% of all CdLS patients harbor a pathogenic variant in one of the five known CdLS genes (Boyle et al. 2014). This test does not detect large deletions or duplications spanning one or more exons.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 CREBBP$690.00 81406 Add to Order
EP300$690.00 81479
FGFR1$690.00 81479
FGFR2$690.00 81479
FGFR3$690.00 81479
NIPBL$690.00 81479
SMC1A$690.00 81479
SMC3$690.00 81479
SRCAP$690.00 81479
Full Panel Price* $840.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (9) $840.00 81406, 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

Only five documented pathogenic variants in FGFR2 are large deletions/insertions (Human Gene Mutation Database; Bochukova et al. 2009). To date, no gross deletions or duplications have been reported in FGFR3 (Human Gene Mutation Database). 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). There are no reported large deletions or duplications in SMC3 (Human Gene Mutation Database).

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Clinical Features

Facial dysostosis is a group of congenital craniofacial anomalies caused by abnormal development of the first and second pharyngeal arches during embryogenesis. This test combines four smaller panels which cover following disorders:

1: Craniosynostosis and Related Disorders: Achondroplasia, Hypochondroplasia, Thanatophoric dysplasia, Crouzon syndrome, Apert syndrome, CATSHL syndrome, Muenke syndrome, Pfeiffer syndrome, Osteoglophonic dysplasia, Jackson-Weiss syndrome, Hartsfield syndrome, LADD syndrome, Saethre-Chotzen syndrome, and Bent bone dysplasia syndrome.

2: Treacher Collins syndrome, Mandibulofacial Dysostosis/, Miller syndrome and Acrofacial dysostosis, Nager type

3: Cornelia de Lange Syndrome

4: Rubinstein-Taybi syndrome and Floating-Harbor Syndrome

Genetics

This NextGen test analyzes multiple genes involved in Facial dysostosis related disorders as described in the clinical section.

Craniosynostosis and Related Disorders:  FGFR1, FGFR2, FGFR3, TWIST1 and TCF12. These disorders are mainly inherited in an autosomal dominant manner, except for FGFR3-related CATSHL syndrome and FGFR1-relared Hartsfield syndrome, which can be inherited either in an autosomal dominant manner (mainly)  or autosomal recessive manner. There is at least one reported autosomal recessive FGFR3-related CATSHL family and two reported FGFR1-related Hartsfield syndrome cases, respectively (Simonis et al. 2013; Makrythanasis et al. 2014).

Treacher Collins Syndrome: TCOF1, POLR1C, POLR1D. TCOF1-related Treacher Collins Syndrome is inherited in an autosomal dominant manner, while POLR1C-related Treacher Collins Syndrome is inherited in autosomal recessive manner. POLR1D related Treacher Collins Syndrome is mainly inherited in an autosomal dominant manner, except for two reported cases showed autosomal recessive inheritance.

Mandibulofacial Dysostosis: EFTUD2.  Autosomal dominant.

Miller Syndrome: DHODH.  Autosomal recessive.

Acrofacial dysostosis, Nager type: SF3B4.  Autosomal dominant

Cornelia de Lange Syndrome (CdLS):  NIPBL, SMC3, SMC1A, RAD21 and HDAC8. NIPBL, SMC3, and RAD21-related CdLS are inherited in autosomal dominant manner. SMC1A-related CdLSis inherited in an X-linked dominant manner (Deardorff et al. 2007). HDAC8-related CdLS is inherited in an X-linked manner, some HDAC8 heterozygous female carriers can be affected due to random X-inactivation (Deardorff et al. 2012).

Rubinstein-Taybi Syndrome: CREBBP and EP300. Autosomal dominant.

Floating-Harbor Syndrome: SRCAP. Autosomal dominant.

See individual gene test descriptions for information on clinical features of these disorders and molecular biology of gene products.

Testing Strategy

 The NextGen Sequencing Panel analyzes 19 Facial Dysostosis genes. They are: FGFR1, FGFR2, FGFR3, TWIST1, TCF12, TCOF1, POLR1C, POLR1D, EFTUD2, DHODH, SF3B4, NIPBL, SMC3, SMC1A, RAD21, HDAC8, CREBBP, EP300 and SRCAP.

For this NGS panel, the full coding regions, plus ~20bp of non-coding DNA flanking each exon, are sequenced for each of the genes. 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.

FGFR1, FGFR2, FGFR3, TCOF1, POLR1C, POLR1D, EFTUD2, DHODH, NIPBL, SMC3, SMC1A, RAD21, and HDAC8 genes can also be tested using our Sanger sequencing assays.

FGFR2, FGFR3, NIPBL, SMC3, and SMC1A genes can be tested by our Deletion/Duplication assay.

Indications for Test

Candidates for this test are patients with clinical and radiologic features consistent with Facial dysostosis related disorders.

Genes

Official Gene Symbol OMIM ID
CREBBP 600140
DHODH 126064
EFTUD2 603892
EP300 602700
FGFR1 136350
FGFR2 176943
FGFR3 134934
HDAC8 300269
NIPBL 608667
POLR1C 610060
POLR1D 613715
RAD21 606462
SF3B4 605593
SMC1A 300040
SMC3 606062
SRCAP 611421
TCF12 600480
TCOF1 606847
TWIST1 601622
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
Achondroplasia 100800
Acrofacial Dysostosis 1, Nager Type 154400
Apert Syndrome 101200
Bent bone dysplasia syndrome 614592
Camptodactyly, Tall Stature, And Hearing Loss Syndrome 610474
Cornelia de Lange syndrome 1 122470
Cornelia de Lange syndrome 2 300590
Cornelia de Lange syndrome 3 610759
Cornelia de Lange syndrome 4 614701
Cornelia de Lange syndrome 5 300882
Craniosynostosis 3 615314
Craniosynostosis, Type 1 123100
Crouzon Syndrome 123500
Crouzon Syndrome With Acanthosis Nigricans 612247
Floating-Harbor Syndrome 136140
Hartsfield syndrome 615465
Hypochondroplasia 146000
Jackson-Weiss Syndrome 123150
Lacrimoauriculodentodigital Syndrome 149730
Mandibulofacial dysostosis, Guion-Almeida type 610536
Miller Syndrome 263750
Muenke Syndrome 602849
Osteoglophonic Dysplasia 166250
Pfeiffer Syndrome 101600
Rubinstein-Taybi Syndrome 180849
Rubinstein-Taybi Syndrome 2 613684
Saethre-Chotzen Syndrome 101400
Thanatophoric Dysplasia Type 1 187600
Thanatophoric Dysplasia Type 2 187601
Treacher Collins Syndrome 154500
Treacher Collins Syndrome 2 613717
Treacher Collins syndrome 3 248390
Trigonocephaly, Nonsyndromic 190440

Related Tests

Name
FGFR1-Related Disorders via the FGFR1 Gene
FGFR2-Related Disorders via the FGFR2 Gene
FGFR3-Related Disorders via the FGFR3 Gene
Achondroplasia via the FGFR3 Gene, Exon 10
Acrofacial Dysostosis 1, Nagar Type via the SF3B4 Gene
Congenital Abnormalities of the Kidney and Urinary Tract (CAKUT) Sequencing Panel with CNV Detection
Cornelia de Lange Syndrome Sequencing Panel
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
Craniosynostosis and Related Disorders Sequencing Panel
Craniosynostosis via the TCF12 Gene
Floating-Harbor Syndrome via the SRCAP Gene
Hypochondroplasia via the FGFR3 Gene
Mandibulofacial Dysostosis, Guion-Almeida Type via the EFTUD2 Gene
Miller Syndrome via the DHODH Gene
Rubinstein-Taybi Syndrome and Floating-Harbor Syndrome Sequencing Panel
Rubinstein-Taybi Syndrome via the CREBBP Gene
Rubinstein-Taybi Syndrome via the EP300 Gene
Saethre-Chotzen Syndrome Via the TWIST1 Gene
Short Rib Skeletal Dysplasia Sequencing Panel
Thanatophoric Dysplasia (TD) via the FGFR3 Gene
Treacher Collins Syndrome via the POLR1C Gene
Treacher Collins Syndrome via the POLR1D Gene
Treacher Collins Syndrome via the TCOF1 Gene
Treacher Collins Syndrome/ Mandibulofacial Dysostosis/Miller syndrome/Acrofacial Dysostosis, Nagar Type Sequencing Panel
X-Linked Intellectual Disability Sequencing Panel with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Baquero-Montoya C, Gil-Rodríguez M c., Teresa-Rodrigo M e., Hernández-Marcos M, Bueno-Lozano G, Bueno-Martínez I, Remeseiro S, Fernández-Hernández R, Bassecourt-Serra M, Rodríguez de Alba M, Queralt E, Losada A, et al. 2014. Could a patient with SMC1A duplication be classified as a human cohesinopathy? Clin Genet 85: 446–451. PubMed ID: 23683030
  • Bernier FP, Caluseriu O, Ng S, Schwartzentruber J, Buckingham KJ, Innes AM, Jabs EW, Innis JW, Schuette JL, Gorski JL, Byers PH, Andelfinger G, Siu V, Lauzon J, Fernandez BA, McMillin M, Scott RH, Racher H; FORGE Canada Consortium, Majewski J, Nickerson DA, Shendure J, Bamshad MJ, Parboosingh JS. 2012. Haploinsufficiency of SF3B4, a Component of the Pre-mRNA Spliceosomal Complex, Causes Nager Syndrome. Am J Hum Genet 90: 925-933. PubMed ID: 22541558
  • Bochukova EG, Roscioli T, Hedges DJ, Taylor IB, Johnson D, David DJ, Deininger PL, Wilkie AOM. 2009. Rare mutations of FGFR2 causing apert syndrome: identification of the first partial gene deletion, and an Alu element insertion from a new subfamily. Hum. Mutat. 30: 204–211. PubMed ID: 18726952
  • Bowman M, Oldridge M, Archer C, O’Rourke A, McParland J, Brekelmans R, Seller A, Lester T. 2012. Gross deletions in TCOF1 are a cause of Treacher–Collins–Franceschetti syndrome. European Journal of Human Genetics 20: 769–777. PubMed ID: 22317976
  • Boyle M i., Jespersgaard C, Brøndum-Nielsen K, Bisgaard A-M, Tümer Z. 2014. Cornelia de Lange syndrome. Clin Genet n/a-n/a. PubMed ID: 25209348
  • Cheng Y-W, Tan CA, Minor A, Arndt K, Wysinger L, Grange DK, Kozel BA, Robin NH, Waggoner D, Fitzpatrick C, Das S, Gaudio D del. 2014. Copy number analysis of NIPBL in a cohort of 510 patients reveals rare copy number variants and a mosaic deletion. Mol Genet Genomic Med 2: 115-123. PubMed ID: 24689074
  • Dauwerse JG, Dixon J, Seland S, Ruivenkamp CAL, Haeringen A van, Hoefsloot LH, Peters DJM, Boers AC, Daumer-Haas C, Maiwald R, Zweier C, Kerr B, Cobo AM, Toral JF, Hoogeboom AJ, Lohmann DR, Hehr U, Dixon MJ, Breuning MH, Wieczorek D. 2010. Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nature Genetics 43: 20–22. PubMed ID: 21131976
  • Deardorff MA, Bando M, Nakato R, Watrin E, Itoh T, Minamino M, Saitoh K, Komata M, Katou Y, Clark D, Cole KE, Baere E De, et al. 2012. HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature 489: 313–317. PubMed ID: 22885700
  • Deardorff MA, Kaur M, Yaeger D, Rampuria A, Korolev S, Pie J, Gil-Rodríguez C, Arnedo M, Loeys B, Kline AD, Wilson M, Lillquist K, Siu V, Ramos FJ, Musio A, Jackson LS, Dorsett D, Krantz ID. 2007. Mutations in Cohesin Complex Members SMC3 and SMC1A Cause a Mild Variant of Cornelia de Lange Syndrome with Predominant Mental Retardation. The American Journal of Human Genetics 80: 485–494. PubMed ID: 17273969
  • Gilissen C, Hehir-Kwa JY, Thung DT, Vorst M van de, Bon BWM van, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A, Leach R, Klein R, Tearle R, Bo T, Pfundt R, Yntema HG, de Vries BB, Kleefstra T, Brunner HG, Vissers LE, Veltman JA. 2014. Genome sequencing identifies major causes of severe intellectual disability. Nature 511: 344-347. PubMed ID: 24896178
  • Gordon CT, Petit F, Oufadem M, Decaestecker C, Jourdain A-S, Andrieux J, Malan V, Alessandri J-L, Baujat G, Baumann C, Boute-Benejean O, Caumes R, Delobel B, Dieterich K, Gaillard D, Gonzales M, Lacombe D, Escande F, Manouvrier-Hanu S, Marlin S, Mathieu-Dramard M, Mehta SG, Simonic I, Munnich A, Vekemans M, Porchet N, de Pontual L, Sarnacki S, Attie-Bitach T, Lyonnet S, Holder-Espinasse M, Amiel J. 2012. EFTUD2 haploinsufficiency leads to syndromic oesophageal atresia. Journal of Medical Genetics 49: 737-746. PubMed ID: 23188108
  • Human Gene Mutation Database (Bio-base).
  • Katsanis SH, Jabs EW. 2012. Treacher Collins 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: 20301704
  • Le Goff C, Mahaut C, Bottani A, Doray B, Goldenberg A, Moncla A, Odent S, Nitschke P, Munnich A, Faivre L, Cormier-Daire V. 2013. Not All Floating-Harbor Syndrome Cases are Due to Mutations in Exon 34 of SRCAP. Human Mutation 34: 88–92. PubMed ID: 22965468
  • Lines, M. A. et al., (2012). PubMed ID: 22305528
  • Makrythanasis P, Temtamy S, Aglan MS, Otaify GA, Hamamy H, Antonarakis SE. 2014. A Novel Homozygous Mutation in FGFR3 Causes Tall Stature, Severe Lateral Tibial Deviation, Scoliosis, Hearing Impairment, Camptodactyly, and Arachnodactyly. Human Mutation 35: 959-963. PubMed ID: 24864036
  • Need, A. C. et al., (2012). PubMed ID: 22581936.
  • Paumard-Hernández B, Berges-Soria J, Barroso E, Rivera-Pedroza CI, Pérez-Carrizosa V, Benito-Sanz S, López-Messa E, Santos F, García-Recuero II, Romance A, Ballesta-Martínez JM, López-González V, Campos-Barros A, Cruz J5, Guillén-Navarro E, Sánchez Del Pozo J, Lapunzina P, García-Miñaur S, Heath KE. 2014. Expanding the mutation spectrum in 182 Spanish probands with craniosynostosis: identification and characterization of novel TCF12 variants. European Journal of Human Genetics. PubMed ID: 25271085
  • Rainger J, Bengani H, Campbell L, Anderson E, Sokhi K, Lam W, Riess A, Ansari M, Smithson S, Lees M, Mercer C, McKenzie K, Lengfeld T, Gener Querol B, Branney P, McKay S, Morrison H, Medina B, Robertson M, Kohlhase J, Gordon C, Kirk J, Wieczorek D, Fitzpatrick DR. 2012. Miller (Genee-Wiedemann) syndrome represents a clinically and biochemically distinct subgroup of postaxial acrofacial dysostosis associated with partial deficiency of DHODH. Human Molecular Genetics 21: 3969-3983. PubMed ID: 22692683
  • Robin NH, Falk MJ, Haldeman-Englert CR. 2011. FGFR-Related Craniosynostosis Syndromes. 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: 20301628
  • Sharma VP, Fenwick AL, Brockop MS, McGowan SJ, Goos JAC, Hoogeboom AJM, Brady AF, Jeelani NO, Lynch SA, Mulliken JB, Murray DJ, Phipps JM, Sweeney E, Tomkins SE, Wilson LC, Bennett S, Cornall RJ, Broxholme J, Kanapin A; 500 Whole-Genome Sequences (WGS500) Consortium, Johnson D, Wall SA, van der Spek PJ, Mathijssen IM, Maxson RE, Twigg SR, Wilkie AO. 2013. Mutations in TCF12, encoding a basic helix-loop-helix partner of TWIST1, are a frequent cause of coronal craniosynostosis. Nat Genet 45: 304-307. PubMed ID: 23354436
  • Simonis N, Migeotte I, Lambert N, Perazzolo C, Silva DC de, Dimitrov B, Heinrichs C, Janssens S, Kerr B, Mortier G, Vliet G Van, Lepage P, Casimir G, Abramowicz M, Smits G, Vilain C. 2013. FGFR1 mutations cause Hartsfield syndrome, the unique association of holoprosencephaly and ectrodactyly. Journal of Medical Genetics 50: 585–592. PubMed ID: 23812909
  • Stef M, Simon D, Mardirossian B, Delrue M-A, Burgelin I, Hubert C, Marche M, Bonnet F, Gorry P, Longy M, Lacombe D, Coupry I, Arveiler B. 2007. Spectrum of CREBBP gene dosage anomalies in Rubinstein–Taybi Syndrome patients. Eur J Hum Genet 15: 843–847. PubMed ID: 17473832
  • Stevens CA. 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
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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