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X-Linked Intellectual Disability Sequencing Panel with CNV Detection

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

Sequencing with CNV

Test Code Test Copy GenesCPT Code Copy CPT Codes
2675 ABCD1 81405,81479 Add to Order
ACSL4 81479,81479
AFF2 81479,81479
AGTR2 81479,81479
AIFM1 81479,81479
ALG13 81479,81479
AMMECR1 81479,81479
AP1S2 81479,81479
ARHGEF6 81479,81479
ARHGEF9 81479,81479
ARSE 81479,81479
ARX 81404,81403
ATP6AP2 81479,81479
ATP7A 81479,81479
ATRX 81479,81479
BCAP31 81479,81479
BCOR 81479,81479
BCORL1 81479,81479
BRWD3 81479,81479
CASK 81479,81479
CCDC22 81479,81479
CDK16 81479,81479
CDKL5 81406,81405
CLCN4 81479,81479
CNKSR2 81479,81479
CUL4B 81479,81479
DCX 81405,81479
DDX3X 81479,81479
DKC1 81479,81479
DLG3 81479,81479
DMD 81408,81161
EBP 81479,81479
EIF2S3 81479,81479
FAAH2 81479,81479
FANCB 81479,81479
FGD1 81479,81479
FLNA 81479,81479
FMR1 81479,81479
FRMPD4 81479,81479
FTSJ1 81406,81405
GDI1 81479,81479
GK 81479,81479
GPC3 81479,81479
GRIA3 81479,81479
HCCS 81479,81479
HCFC1 81479,81479
HDAC6 81479,81479
HDAC8 81479,81479
HMGB3 81479,81479
HNRNPH2 81479,81479
HPRT1 81479,81479
HSD17B10 81479,81479
HUWE1 81479,81479
IDS 81405,81479
IGBP1 81479,81479
IKBKG 81479,81479
IL1RAPL1 81479,81479
IQSEC2 81479,81479
KDM5C 81407,81479
KDM6A 81479,81479
KIF4A 81479,81479
KLHL15 81479,81479
L1CAM 81407,81479
LAMP2 81405,81479
LAS1L 81479,81479
MAOA 81479,81479
MBTPS2 81479,81479
MECP2 81302,81304
MED12 81479,81479
MID1 81479,81479
MID2 81479,81479
MSL3 81479,81479
MTM1 81405,81479
NAA10 81479,81479
NDP 81404,81403
NDUFA1 81404,81479
NEXMIF 81479,81479
NHS 81479,81479
NLGN3 81405,81479
NLGN4X 81405,81404
NONO 81479,81479
NSDHL 81479,81479
OCRL 81479,81479
OFD1 81479,81479
OGT 81479,81479
OPHN1 81479,81479
OTC 81405,81479
PAK3 81479,81479
PCDH19 81405,81479
PDHA1 81406,81405
PGK1 81479,81479
PHF6 81479,81479
PHF8 81479,81479
PIGA 81479,81479
PLP1 81405,81404
POLA1 81479,81479
PORCN 81479,81479
PQBP1 81405,81404
PRPS1 81479,81479
PTCHD1 81479,81479
RAB39B 81479,81479
RBM10 81479,81479
RLIM 81479,81479
RNF113A 81479,81479
RPL10 81479,81479
RPS6KA3 81479,81479
SHROOM4 81479,81479
SLC16A2 81405,81404
SLC35A2 81479,81479
SLC6A8 81479,81479
SLC9A6 81406,81479
SMC1A 81479,81479
SMS 81479,81479
SOX3 81479,81479
SRPX2 81479,81479
SSR4 81479,81479
STAG2 81479,81479
SYN1 81479,81479
SYP 81479,81479
TAF1 81479,81479
THOC2 81479,81479
TIMM8A 81479,81479
TMLHE 81479,81479
TSPAN7 81479,81479
UBE2A 81479,81479
UPF3B 81479,81479
USP27X 81479,81479
USP9X 81479,81479
WDR45 81479,81479
ZC4H2 81479,81479
ZDHHC9 81479,81479
ZMYM3 81479,81479
ZNF711 81479,81479
Full Panel Price* $1310
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
2675 Genes x (133) $1310 81161, 81302, 81304, 81403(x2), 81404(x7), 81405(x15), 81406(x4), 81407(x2), 81408, 81479(x232) Add to Order

New York State Approved Test

Pricing Comments

CPT codes 81470 and 81471 can be used if at least 60 of the genes in the panel are analyzed. We are happy to accommodate requests for testing single genes in this panel 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 via our PGxome Custom Panel tool.

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 26 days.

Clinical Sensitivity

Genes located on the X chromosome represent ~15% of the total genes currently known to cause intellectual disability (ID) in humans (Neri et al. 2018. PubMed ID: 29696803). Based on our own past results for this panel, which are in-line with published cohorts, we estimate this panel will identify pathogenic variants in 20-40% of patients with a family history of X-linked intellectual disability (XLID), who are fragile-X negative. Increased diagnostic yield is observed for syndromic cases, while lower rates are observed for isolated or nonsyndromic ID (de Brouwer et al. 2007. PubMed ID: 17221867; Hu et al. 2016. PubMed ID: 25644381; Chiurazzi and Pirozzi. 2016. PubMed ID: 27127621). Pathogenic variants in over 140 genes have been associated with XLID (Neri et al. 2018. PubMed ID: 29696803). Due to this high genetic heterogeneity, testing a large panel of genes is known to have a higher diagnostic yield (Vissers et al. 2016. PubMed ID: 26503795). This test will detect both large copy number variants (CNVs) as well as smaller sequence variants (SNVs) with high analytical sensitivity. Detection of trinucleotide repeat expansions (as seen in fragile X syndrome for example) requires an alternate test.

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Clinical Features

Intellectual Disability (ID) is characterized by significant limitations in intellectual functioning and impairments in adaptive behavior, manifesting before 18 years of age (American Association of Intellectual and Developmental Disabilities, AAIDD). Intellectual functioning is assessed using an intelligence quotient (IQ) test, and a cutoff of ≤70 is considered intellectually impaired. Adaptive behavior is assessed across three domains - conceptual, social, and practical abilities (AAIDD). ID is diagnosed in ~1-3% of the total population, and X-linked genes account for ~5-10% of ID cases in males (Vissers et al. 2016. PubMed ID: 26503795; Kaufman et al. 2010. PubMed ID: 21124998; Lubs et al. 2012. PubMed ID: 22482801; Tzschach. 2015. PubMed ID: 25649377). X-linked intellectual disability (XLID) is phenotypically diverse, with conditions ranging from severe, early onset syndromic diseases involving multiple systems, to mild nonsyndromic forms (Neri et al. 2018. PubMed ID: 29696803).

While true treatments are often limited for XLID disorders, advantages of testing and molecular diagnosis are still numerous. These include prognostic information, early identification and treatment of symptoms (autism, seizures, comorbidities), and ability to join condition-specific support groups. When parental inheritance is observed, families can use this information for future family planning (including prenatal testing or pre-implantation genetic diagnosis). Alternatively, if a patient has a confirmed de novo variant (undetectable in parents), this may ease anxiety on the family, due to the dramatically reduced recurrence risk.

Genetics

X-linked intellectual disability occurs in both X-linked dominant and X-linked recessive inheritance patterns. Males are disproportionately affected with X-linked recessive (XLR) forms of XLID due to hemizygosity of the X-chromosome, while several factors affect disease presentation in females. One of these factors is skewed X-chromosome inactivation patterns in females, which can impact disease severity or alter presenting symptoms (Plenge et al. 2002. PubMed ID: 12068376; Fieremans et al. 2016. PubMed ID: 27159028). In cases where inactivation is skewed completely toward the mutated allele, an XLR disorder may present similarly in a female to that seen in male. Alternatively, skewing toward the normal allele or tissue specific patterns of skewing may cause female carriers of an X-linked dominant disorder to present with significantly milder or variable presentations. The cellular mosaicism resulting from random X-inactivation in females is proposed as the mechanism for one female-limited form of XLID, caused by pathogenic variation in the PCDH19 gene (Dibbens et al. 2008. PubMed ID: 18469813). Another factor affecting gender-skewing in X-linked disorders is early lethality in males for some X-linked diseases, leading to these disorders appearing to disproportionately affect females (Franco et al. 2006. PubMed ID: 16650755).

This panel focuses on genes associated with established monogenic forms of XLID (Neri et al. 2018. PubMed ID: 29696803). A wide variety of causative variant types in these genes have been reported to cause XLID (including missense, nonsense, splicing, frameshift, large insertions and deletions, complex rearrangements, and trinucleotide repeat expansions)(Human Gene Mutation Database). Causative XLID variants in males are frequently inherited from an unaffected or mildly affected mother; yet, de novo mutations are another common cause of XLID in both males and females.

Testing Strategy

For this Next Generation Sequencing (NGS) test, sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments.

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.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

This panel typically provides 97.9% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing.

Genes of this panel that are likely to get low coverage in an area of high pathogenic variation include (but are not necessarily limited to): ABCD1, IKBKG, and RPS6KA3. If a disorder associated with one of these genes is suspected, additional testing may be warranted.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

This panel is recommended for patients with syndromic or nonsyndromic intellectual disability, and a family history suggestive of an X-linked pattern of inheritance. Fragile X repeat expansion testing is recommended in addition to this test.

Genes

Official Gene Symbol OMIM ID
ABCD1 300371
ACSL4 300157
AFF2 300806
AGTR2 300034
AIFM1 300169
ALG13 300776
AMMECR1 300195
AP1S2 300629
ARHGEF6 300267
ARHGEF9 300429
ARSE 300180
ARX 300382
ATP6AP2 300556
ATP7A 300011
ATRX 300032
BCAP31 300398
BCOR 300485
BCORL1 300688
BRWD3 300553
CASK 300172
CCDC22 300859
CDK16 311550
CDKL5 300203
CLCN4 302910
CNKSR2 300724
CUL4B 300304
DCX 300121
DDX3X 300160
DKC1 300126
DLG3 300189
DMD 300377
EBP 300205
EIF2S3 300161
FAAH2 300654
FANCB 300515
FGD1 300546
FLNA 300017
FMR1 309550
FRMPD4 300838
FTSJ1 300499
GDI1 300104
GK 300474
GPC3 300037
GRIA3 305915
HCCS 300056
HCFC1 300019
HDAC6 300272
HDAC8 300269
HMGB3 300193
HNRNPH2 300610
HPRT1 308000
HSD17B10 300256
HUWE1 300697
IDS 300823
IGBP1 300139
IKBKG 300248
IL1RAPL1 300206
IQSEC2 300522
KDM5C 314690
KDM6A 300128
KIF4A 300521
KLHL15 300980
L1CAM 308840
LAMP2 309060
LAS1L 300964
MAOA 309850
MBTPS2 300294
MECP2 300005
MED12 300188
MID1 300552
MID2 300204
MSL3 300609
MTM1 300415
NAA10 300013
NDP 300658
NDUFA1 300078
NEXMIF 300524
NHS 300457
NLGN3 300336
NLGN4X 300427
NONO 300084
NSDHL 300275
OCRL 300535
OFD1 300170
OGT 300255
OPHN1 300127
OTC 300461
PAK3 300142
PCDH19 300460
PDHA1 300502
PGK1 311800
PHF6 300414
PHF8 300560
PIGA 311770
PLP1 300401
POLA1 312040
PORCN 300651
PQBP1 300463
PRPS1 311850
PTCHD1 300828
RAB39B 300774
RBM10 300080
RLIM 300379
RNF113A 300951
RPL10 312173
RPS6KA3 300075
SHROOM4 300579
SLC16A2 300095
SLC35A2 314375
SLC6A8 300036
SLC9A6 300231
SMC1A 300040
SMS 300105
SOX3 313430
SRPX2 300642
SSR4 300090
STAG2 300826
SYN1 313440
SYP 313475
TAF1 313650
THOC2 300395
TIMM8A 300356
TMLHE 300777
TSPAN7 300096
UBE2A 312180
UPF3B 300298
USP27X 300975
USP9X 300072
WDR45 300526
ZC4H2 300897
ZDHHC9 300646
ZMYM3 300061
ZNF711 314990
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
2-Methyl-3-Hydroxybutyric Aciduria XL 300438
Aarskog Syndrome XL 305400
Adrenoleukodystrophy XL 300100
Allan-Herndon-Dudley Syndrome XL 300523
Alpha-Thalassemia Myelodysplasia Syndrome XL 300448
Arts Syndrome XL 301835
Asperger Syndrome, X-Linked, Susceptibility To, 1 XL 300494
Asperger Syndrome, X-Linked, Susceptibility To, 2 XL 300497
ATR-X Syndrome XL 301040
Autism, Susceptibility To, X-Linked 1 XL 300425
Autism, Susceptibility To, X-Linked 2 XL 300495
Autism, Susceptibility To, X-Linked 3 XL 300496
Autism, Susceptibility to, X-linked 4 XL 300830
Autism, Susceptibility To, X-Linked 5 XL 300847
Autism, Susceptibility to, X-linked 6 XL 300872
Becker Muscular Dystrophy XL 300376
Borjeson-Forssman-Lehmann Syndrome XL 301900
Cardiac Valvular Dysplasia, X-Linked XL 314400
Cardiomyopathy, Dilated, 3B XL 302045
Cataract, Congenital, X-Linked XL 302200
Cerebral Creatine Deficiency Syndrome 1 XL 300352
Charcot-Marie-Tooth Disease, X-Linked Recessive, Type 5 XL 311070
Child Syndrome XL 308050
Chondrodysplasia Punctata 1, X-Linked Recessive XL 302950
Chondrodysplasia Punctata 2 X-Linked Dominant XL 302960
Chondrodysplasia with Platyspondyly, Distinctive Brachydactyly, Hydrocephaly, and Microphthalmia XL 300863
CK syndrome XL 300831
Coffin-Lowry Syndrome XL 303600
Combined Oxidative Phosphorylation Deficiency 6 XL 300816
Congenital Disorder of Glycosylation Type IIm XL 300896
Congenital Disorder of Glycosylation Type Iy XL 300934
Cornelia de Lange syndrome 2 XL 300590
Cornelia de Lange syndrome 5 XL 300882
Corpus Callosum, Agenesis Of, With Mental Retardation, Ocular Coloboma, And Micrognathia XL 300472
Corpus Callosum, Partial Agenesis Of, X-Linked XL 304100
Cowchock Syndrome XL 310490
Danon Disease XL 300257
Deafness, Dystonia, and Cerebral Hypomyelination XL 300475
Deafness, X-Linked 1 XL 304500
Deafness, X-Linked 5 XL 300614
Dent Disease 2 XL 300555
Duchenne Muscular Dystrophy XL 310200
Dyskeratosis Congenita X-Linked XL 305000
Dystonia 3, Torsion, X-Linked XL 314250
Ectodermal Dysplasia, Anhidrotic, With Immunodeficiency, Osteopetrosis, And Lymphedema XL 300301
Encephalopathy, Neonatal Severe, Due To Mecp2 Mutations XL 300673
Epilepsy, X-Linked, With Variable Learning Disabilities And Behavior Disorders XL 300491
Epileptic encephalopathy, early infantile, 1 XL 308350
Epileptic Encephalopathy, Early Infantile, 2 XL 300672
Epileptic Encephalopathy, Early Infantile, 36 XL 300884
Epileptic Encephalopathy, Early Infantile, 8 XL 300607
Epileptic Encephalopathy, Early Infantile, 9 XL 300088
Exudative Vitreoretinopathy 2, X-Linked XL 305390
Fanconi Anemia, Complementation Group B XL 300514
Fg Syndrome XL 305450
FG Syndrome 2 XL 300321
Focal Dermal Hypoplasia XL 305600
Fragile X Syndrome XL 300624
Fragile X Tremor/Ataxia Syndrome XL 300623
Frontometaphyseal Dysplasia XL 305620
Glycerol Kinase Deficiency XL 307030
Gout, HPRT-Related XL 300323
Hypohidrotic Ectodermal Dysplasia With Immune Deficiency XL 300291
Ichthyosis Follicularis Atrichia Photophobia Syndrome XL 308205
Immunodeficiency Without Anhidrotic Ectodermal Dysplasia XL 300584
Incontinentia Pigmenti XL 308300
Intestinal Pseudoobstruction Neuronal Chronic Idiopathic X-Linked XL 300048
Invasive Pneumococcal Disease, Recurrent Isolated, 2 XL 300640
Joubert Syndrome 10 XL 300804
Kabuki Syndrome 2 XL 300867
Keratosis Follicularis Spinulosa Decalvans XL 308800
Lenz Microphthalmia Syndrome XL 309800
Lesch-Lyhan Syndrome XL 300322
Lowe Syndrome XL 309000
Lujan-Fryns Syndrome XL 309520
MECP2 Duplication Syndrome XL 300260
MEHMO Syndrome XL 300148
Melnick-Needles Syndrome XL 309350
MEND Syndrome XL 300960
Menkes Kinky-Hair Syndrome XL 309400
Mental Retardation 105 XL 300984
Mental Retardation And Microcephaly With Pontine And Cerebellar Hypoplasia XL 300749
Mental Retardation, with or without Nystagmus XL 300422
Mental Retardation, X-Linked 1/78 XL 309530
Mental Retardation, X-linked 100 XL 300923
Mental Retardation, X-linked 101 XL 300928
Mental Retardation, X-Linked 102 XL 300958
Mental Retardation, X-linked 103 XL 300982
Mental Retardation, X-linked 104 XL 300983
Mental retardation, X-linked 106 XL 300997
Mental Retardation, X-linked 12/35 XL 300957
Mental Retardation, X-Linked 19 XL 300844
Mental Retardation, X-Linked 21 XL 300143
Mental Retardation, X-Linked 3 (Methylmalonic Acidemia and Homocysteinemia, cblX Type) XL 309541
Mental Retardation, X-Linked 30 XL 300558
Mental Retardation, X-Linked 41 XL 300849
Mental Retardation, X-Linked 46 XL 300436
Mental Retardation, X-linked 49 XL 300114
Mental Retardation, X-Linked 58 XL 300210
Mental Retardation, X-linked 61 XL 300978
Mental Retardation, X-Linked 63 XL 300387
Mental Retardation, X-Linked 72 XL 300271
Mental Retardation, X-Linked 9 XL 309549
Mental Retardation, X-Linked 90 XL 300850
Mental Retardation, X-Linked 93 XL 300659
Mental Retardation, X-Linked 96 XL 300802
Mental Retardation, X-Linked 97 XL 300803
Mental Retardation, X-linked 98 XL 300912
Mental Retardation, X-linked 99 XL 300919
Mental retardation, X-linked 99, Syndromic, Female-Restricted XL 300968
Mental retardation, X-linked syndromic, Turner type XL 309590
Mental Retardation, X-linked, FRAXE Type XL 309548
Mental Retardation, X-Linked, Syndromic 10 XL 300220
Mental Retardation, X-Linked, Syndromic 13 XL 300055
Mental Retardation, X-Linked, Syndromic 14 XL 300676
Mental Retardation, X-linked, Syndromic 33 XL 300966
Mental Retardation, X-linked, Syndromic 34 XL 300967
Mental Retardation, X-linked, Syndromic, 35 XL 300998
Mental Retardation, X-linked, Syndromic, Bain Type XL 300986
Mental Retardation, X-Linked, Syndromic, Christianson Type XL 300243
Mental Retardation, X-Linked, Syndromic, Claes-Jensen Type XL 300534
Mental Retardation, X-Linked, Syndromic, Hedera Type XL 300423
Mental retardation, X-linked, syndromic, Houge type XL 301008
Mental Retardation, X-Linked, Syndromic, Nascimento Type XL 300860
Mental Retardation, X-Linked, Syndromic, Raymond Type XL 300799
Mental Retardation, X-Linked, Syndromic, Wu Type XL 300699
Mental Retardation, X-Linked, With Or Without Seizures, Arx-Related XL 300419
Mental Retardation, X-Linked, With Panhypopituitarism XL 300123
Mental Retardation, X-Linked, With Short Stature, Hypogonadism, And Abnormal Gait XL 300354
Mental Retardation-Hypotonic Facies Syndrome X-Linked, 1 XL 309580
Microphthalmia Syndromic 7 XL 309801
Microphthalmia, Syndromic 13 XL 300915
Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis XL 300990
Mitochondrial complex I deficiency, nuclear type 12 XL 301020
Mohr-Tranebjaerg Syndrome XL 304700
Monoamine Oxidase A Deficiency XL 300615
Mucopolysaccharidosis, MPS-II XL 309900
Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome 2 XL 300868
Nance-Horan Syndrome XL 302350
Neurodegeneration With Brain Iron Accumulation 5 XL 300894
Neurodevelopmental disorder, X-linked, with craniofacial abnormalities XL 301022
Norrie Disease XL 310600
Occipital Horn Syndrome XL 304150
Oculofaciocardiodental Syndrome XL 300166
Ogden Syndrome XL 300855
OHDO Syndrome, X-linked; OHDOX XL 300895
Olmsted syndrome, X-linked XL 300918
Opitz G/BBB Syndrome, Type I XL 300000
Oral-Facial-Digital Syndrome XL 311200
Ornithine Carbamoyltransferase Deficiency XL 311250
Osteogenesis imperfecta, type XIX XL 301014
Oto-Palato-Digital Syndrome Type 1 XL 311300
Oto-Palato-Digital Syndrome, Type II XL 304120
Panhypopituitarism X-Linked XL 312000
Parkinsonism with Spasticity, X-Linked XL 300911
Paroxysmal Nocturnal Hemoglobinuria XL 300818
Partington X-Linked Mental Retardation Syndrome XL 309510
Pelizaeus-Merzbacher Disease XL 312080
Pettigrew Syndrome XL 304340
Phosphoglycerate Kinase 1 Deficiency XL 300653
Phosphoribosylpyrophosphate Synthetase Superactivity XL 300661
Pigmentary Disorder, Reticulate, with Systemic Manifestations, X-linked XL 301220
Premature Ovarian Failure XL 311360
Proud Levine Carpenter Syndrome XL 300004
Pyruvate Dehydrogenase E1-Alpha Deficiency XL 312170
Renpenning Syndrome 1 XL 309500
Retinitis Pigmentosa 23 XL 300424
Rett Syndrome XL 312750
Ritscher-Schinzel Syndrome 2 XL 300963
Severe X-Linked Myotubular Myopathy XL 310400
Siderius X-Linked Mental Retardation Syndrome XL 300263
Simpson-Golabi-Behmel Syndrome XL 312870
Simpson-Golabi-Behmel Syndrome, Type 2 XL 300209
Snyder Robinson Syndrome XL 309583
Spastic Paraplegia 1 XL 303350
Spastic Paraplegia 2 XL 312920
Spinal Muscular Atrophy, Distal, X-Linked 3 XL 300489
Stocco Dos Santos Syndrome XL 300434
TARP Syndrome XL 311900
Terminal Osseous Dysplasia XL 300244
Trichothiodystrophy 5, nonphotosensitive XL 300953
Waisman Syndrome XL 311510
Wieacker-Wolff Syndrome XL 314580
Wilms' Tumor AD 194070
Wilson-Turner syndrome XL 309585
X-Linked Familial Atypical Mycobacteriosis, Type 1 XL 300636
X-Linked Hydrocephalus Syndrome XL 307000
X-Linked Lissencephaly XL 300067
X-Linked Lissencephaly 2 XL 300215
X-Linked Periventricular Heterotopia XL 300049
X-LinkedMental Retardation With Cerebellar Hypoplasia And Distinctive Facial Appearance XL 300486

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CONTACTS

Genetic Counselors
Geneticist
Citations
  • Chiurazzi and Pirozzi. 2016. PubMed ID: 27127621
  • de Brouwer et al. 2007. PubMed ID: 17221867
  • Dibbens et al. 2008. PubMed ID: 18469813
  • Fieremans et al. 2016. PubMed ID: 27159028
  • Franco et al. 2006. PubMed ID: 16650755
  • Hu et al. 2016. PubMed ID: 25644381
  • Human Gene Mutation Database (Bio-base).
  • Kaufman et al. 2010. PubMed ID: 21124998
  • Lubs et al. 2012. PubMed ID: 22482801
  • Neri et al. 2018. PubMed ID: 29696803
  • Plenge et al. 2002. PubMed ID: 12068376
  • Tzschach et al. 2015. PubMed ID: 25649377
  • Vissers et al. 2016. PubMed ID: 26503795
Order Kits
TEST METHODS

Exome Sequencing with CNV Detection

Test Procedure

For PGxome® we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus 10 bases of flanking non-coding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. As required, genomic DNA is extracted from patient specimens. Patient DNA corresponding to these regions is captured using Agilent Clinical Research Exome hybridization probes. Captured DNA is sequenced on the NovaSeq 6000 using 2x150 bp paired-end reads (Illumina, San Diego, CA, USA). The following quality control metrics are generally achieved: >97% of target bases are covered at >20x, and mean coverage of target bases >120x. Data analysis and interpretation is performed by the internally developed software Titanium-Exome. In brief, the output data from the NovaSeq 6000 is converted to fastqs by Illumina Bcl2Fastq, and mapped by BWA. Variant calls are made by the GATK Haplotype caller and annotated using in house software and SnpEff. Variants are filtered and annotated using VarSeq (www.goldenhelix.com).

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.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as aCGH, MLPA, or PCR before they are reported.

Analytical Validity

NextGen Sequencing: 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.

Copy Number Variant Analysis: The PGxome test detects most larger deletions and duplications including intragenic CNVs and large cytogenetic events; however aberrations in a small percentage of regions may not be accurately detected due to sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size (e.g., 1-3 exons vs. 4 or more exons), and inadequate coverage. In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of four exon size or larger is >95%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region.

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 sequencing does not reveal any heterozygous differences from the reference sequence, we cannot be certain that we were able to detect both patient alleles.

For technical reasons, the PGxome test is not 100% sensitive. Some exons cannot be efficiently captured, and some genes cannot be accurately sequenced because of the presence of multiple copies in the genome. Therefore, a small fraction of sequence variants will not be detected.

We sequence coding exons for all available transcripts plus 10 bp of flanking non-coding DNA for each exon. We also sequence other regions within or near genes in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere.  Unless specifically indicated, test reports contain no information about other portions of genes.

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 amplification.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes if taken 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.

Balanced translocations or inversions are only rarely detected.

Certain types of sex chromosome aneuploidy may not be detected.  

Our ability to detect CNVs due to somatic mosaicism is limited.

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.

A negative finding does not rule out a genetic diagnosis.

Genetic counseling to help to explain test results to the patients and to discuss reproductive options is recommended.

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
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