Genetic Testing Details

Insight Medical Genetics is home to a full-service CLIA-licensed and CAP certified cytogenetic genetics laboratory. Highly trained lab technologists provide in-house testing for a wide range of diagnostic and screening tests with particular capacities to handle and process prenatal samples. 

 

Cytogenetic Genetic Testing

Same-Day Fluorescence In Situ Hybridization (FISH)

FISH genetic testing is used to quickly detect many of the most common chromosome abnormalities, such as:

  • Down syndrome

  • Trisomy 18

  • Trisomy 13

  • Sex chromosome abnormalities

When the CVS or amniocentesis sample is received by the laboratory in the morning, IMG can provide same-day FISH results.


Karyotyping

A full chromosome analysis, called a karyotype, is the standard for prenatal diagnosis of chromosome abnormalities, following a CVS or amniocentesis procedure.

Depending on the extent to which the cells need to be grown in culture, it can take up to two business weeks to see results. Insight Medical Genetics will contact providers as soon as the final karyotype is complete.


Chromosome Microarray Analysis

Insight Medical Genetics can also test a CVS or amniocentesis specimen using prenatal chromosome microarray (CMA) analysis. The American Congress of Obstetricians and Gynecologists and the Society for Maternal Fetal Medicine recommend CMA for prenatal diagnosis as the test that can detect the small chromosome abnormalities conventional karyotyping cannot identify.

The Insight microarray panel targets approximately 80 known genetic syndromes associated with microdeletion and microduplication syndromes that may cause birth defects and developmental or intellectual disabilities. The CMA will also evaluate for other deletions, duplications and abnormalities above a 1 Mb threshold.

Insight will perform chromosomal microarray analysis on a specimen obtained by diagnostic procedure following an abnormal ultrasound and/or negative FISH result.

A five-cell karyotype also accompanies all microarray analyses to identify translocations or mosaicism that may be present.


Send-In Specimen for Chromosomal Microarray Analysis

Certain DNA extraction methods may affect the quality of microarray test results. Insight recommends sending either of the following samples:

  • Direct chorionic villi: 15-20mg

  • Direct or cultured amniotic fluid: 2 T-25 flasks of confluent fetal cells

A maternal blood sample is also required to conduct the necessary maternal cell contamination studies prior to all prenatal CMA tests.

POC ANALYSIS: We welcome product of conception (POC) specimens and will perform a combination of karyotype and chromosomal microarray analysis. Please contact us for details, specimen requirements, and turnaround times to meet your needs. Additional guidelines for POC specimens can be found here.

 

Molecular Genetics Testing

Noonan Syndrome Panel

Noonan syndrome (NS) is an autosomal dominant assortment of phenotypic findings characterized by short stature, congenital heart defect, and developmental delay of variable degree. In addition to Noonan syndrome, a variety of other phenotypes, recognized as RASopathies, are associated with mutations in the same genes that are related to Noonan syndrome.  The RASopathies are a group of rare genetic conditions caused by mutations in genes of the Ras-MAPK pathway.  Abnormalities of this pathway have profound effects on development and can cause one of several different syndromes in addition to Noonan syndrome --  Cardio-Facio-Cutaneous (CFC), Costello, Legius, Nerofibromatosis type 1 (NF1), Noonan with Multiple Lentigines (formerly called LEOPARD syndrome).  

The most common predictor of Noonan syndrome in the prenatal period is the finding of a positive first trimester screen – primarily an increased nuchal translucency – with a follow up determination of a normal karyotype following an invasive procedure (CVS or amniocentesis).  The intent of this next generation sequencing panel is to provide a means of diagnosing Noonan syndrome at the molecular level as well as some of the related RASopathies.

This panel includes 12 genes: PTPN11, SOS1, RAF1, KRAS, NRAS, BRAF, MAP2K1, MAP2K2, SHOC2, CBL, HRAS, and RIT1.  By literature review, molecular genetic testing identifies a mutation in PTPN11 in 50% of affected individuals, SOS1 in approximately 13%, RAF1 in 3% to 17%, and KRAS in fewer than 5%. Other genes in which mutations have been reported to cause Noonan syndrome and other RASopathies in fewer than 1% of cases include NRASBRAF, MAP2K1, MAP2K2, CBL, SHOC2, HRAS, and RIT1.  The overall detection rate is 70-85% with the current understanding of the genetic underpinnings of Noonan and related disorders. Insight’s Noonan syndrome next generation sequencing panel, with confirmation by Sanger sequencing, covers all of the coding regions along with +/- 30 base pairs into the flanking intronic regions of these genes with at least 20X coverage, greater than 98% analytic sensitivity, and greater than 99% analytic specificity.


Skeletal Dysplasia Panel

Insight provides prenatal patients with early genetic testing for mutations associated with skeletal dysplasia. Skeletal dysplasia is a category of disorders which are characterized by bone and cartilage abnormalities.  There are over 350 distinct disorders included in this category.  An estimate of 1 in every 4000 births are affected by a form of skeletal dysplasia.  A summary of the genes tested and the conditions associated with pathogenic variants in each gene is included below. It is difficult to calculate a specific detection rate for each condition included in a targeted panel of this kind; however, the proportion of reported disease-causing variants for each gene tested is as high as 99%.

The Skeletal Dysplasia Testing Panel uses next generation sequencing, with confirmation by Sanger sequencing, to test for variants across 19 genes known to be associated with prenatal and/or perinatal onset skeletal dysplasias. All exons in each gene +/-30 base pairs into flanking introns are sequenced for known pathogenic variants with at least 20X coverage, greater than 98% analytic sensitivity, and greater than 99% analytic specificity.  Additionally, previously unreported variants are curated using the criteria of the American College of Medical Genetics criteria (Richards et al, 2015) for classification with respect to predicted clinical impact.  

 

Genes TestedMode of InheritanceConditions associated with mutations in the gene
FGFR3: 4p16.3ADThanatophoric dysplasia
Achondroplasia
Hypochondroplasia
SADDAN dysplasia
Crouzon syndrome
Muenke syndrome
LADD syndrome
CATSHL syndrome
FGFR2: 10q26ADCrouzon syndrome
Pfeiffer syndrome
Jackson-Weiss syndrome
Beare Stevenson syndrome
Apert syndrome
Saethre-Chotzen syndrome
Craniosynostosis (undifferentiated)
FGFR1: 8p11.23ADPfeiffer Syndrome
Osteoglyphonic Dysplasia
Kallman syndrome
COL2A1: 12q13.11-q13.2ADAchondrogenesis type 2
Achondrogenesis/Hypochondrogenesis
Hypochondrogenesis
Spondyloepimetaphyseal dysplasia, Strudwick type
Spondylepiphyseal dysplasia congenita
Spondyloperipheral dysplasia
Platyspondylic skeletal dysplasia, Torrance type
COL1A1: 17q21.33AD/AREhlers-Danlos
Ostepgenesis imperfecta
Caffey Disease
DYNC2H1: 14q32.31AD/ARAsphyxiating thoracic dystrophy
SLC26A2 (DTDST): 5q32-q33.1ARDiastrophic dysplasia
Recessive multiple epiphyseal dysplasia
Achondrogenesis type 1B
Atelosteogenesis type 2
ALPL: 1p36.1-p34ARHypophosphatasia (perinatal type)
ROR2: 9q22ARAutosomal Recessive Robinow syndrome
ESCO2: 8p21.1ARRoberts syndrome
SOX9: 17q24.3-q25.1ADCampomelic dysplasia
TWIST1: 7p21.1ADSaethre-Chotzen Syndrome
EVC: 4p16.2AREllis van Creveld (Weyer’s acrofacial dysostosis)
EVC2: 4p16.2AREllis van Creveld 2
IFT80: 3q25.33ARAsphyxiating thoracic dystrophy
PAM16: 16p13.3ARSpondylometaphyseal Dysplasia (Magarbane-Dagheri-Milki Type)
INPPL1: 11p13.4AROpsismodysplasia
PEX7: 6q23.3ARRhizomelic chondrodysplasia punctate Refsum Disease
AGPS: 2q31.2ARRhizomelic chondrodysplasia punctate 3

Osteogenesis Imperfecta Panel

Osteogenesis Imperfecta (OI) is a clinically and genetically heterogeneous disorder of connective tissue that results in deformity(ies), growth deficiency, and skeletal/bone fragility; it is commonly called the “brittle bone disease.”  Most cases (~90%) of OI have been attributed to mutations in collagen, COL1A1 and COL1A2 more specifically.  Additionally associated genes are: IFITM5, CRTAP, BMP1, PLOD2, PPIB, SERPINF1, SERPINH1, SP7, TMEM38B, WNT1, FKBP10, and LEPRE1.  Insight’s osteogenesis imperfect next generation sequencing panel, with confirmation by Sanger sequencing, covers over 99% of the coding regions along with +/- 30 base pairs into the flanking intronic regions of these genes with at least 20X coverage, greater than 98% analytic sensitivity, and greater than 99% analytic specificity .

Insight recommends OI testing in conjunction with the Skeletal Dysplasia panel when ultrasound findings are unable to differentiate between the two conditions. 

The table below lists the 14 genes in Insight’s OI panel along with the associated OI types, modes of inheritance, and any related disorders with known mutations in each genes.

GeneOI Type(s)*Inheritance**Other Disorder(s)
COL1A1I, II, Ill, IVADCaffey Disease, Ehlers-Danlos Syndrome (AD)
COL1A2I, II, Ill, IVADEhlers-Danlos Syndrome (AR/AD)
BMP1IIAR
LEPRE1II, IIIAR
PPIBII, IIIAR
CRTAPII, III, IVAR
SERPINH1IIIAR
SERPINF1III, IVAR
WNT1III, IVAR/AD
FKBP10IVARBruck Syndrome I
SP7IVAR
TMEM38BIVAR
IFITM5VAD
PLOD2ARBruck Syndrome II
*Classification according to Warman, et al (2010)
**AD= Autosomal Dominant, AR = Autosomal Recessive

Fragile X Syndrome

Fragile X syndrome is associated with the FMR1 gene and is the most common form of inherited intellectual disability.  Fragile X testing is used to determine the number of CGG trinucleotide repeats, an unstable genetic sequence that expands from one generation to the next.

The analysis of the FMR1 gene at Insight includes both an assessment of the CGG repeat number and the methylation status of the promoter, the latter of particular importance for a complete evaluation when a full mutation is detected.

FMR1 mutations are associated with fragile X syndrome, fragile X tremor/ataxia syndrome (FXTAS), and premature ovarian failure (FXPOI). The results of an FMR1 analysis are divided into four categories: normal range (6-44 repeats), intermediate zone (45-54 repeats), premutation (55-200 repeats),  and full mutation (>200 repeats).

Insight will perform fragile X testing on prenatal samples as well as blood specimens from adults.


Spinal Muscular Atrophy Testing

Spinal muscular atrophy (SMA) is a progressive neurologic condition primarily associated with the SMN1 gene. SMA can lead to an early infant death, though some children won’t show signs of the disease for several years.

The vast majority of people who are affected with SMA have a deletion in both copies of the SMN1 gene that leads to a non-functioning protein.  This accounts for ~95% of cases of SMA.  There are also instances of point mutations that contribute to the incidence of SMA, and taken together with the deletion-based cause account for 98-99% of SMA cases.  The remaining 1-2% are due to an unusual configuration of the SMN1 gene.

SMA is inherited as an autosomal recessive condition, which means that only when both parents are carriers, there is a 25 percent chance of their child being born with SMA. Because of the frequency of SMA, approximately 1 in 40-65 depending on the ethnic background of the population and the ability to test for carriers of an altered SMN1 gene, the American College of Medical Genetics recommends that all prospective parents be screened.  

Insight offers both deletion testing and point mutation screening for adults as well as prenatal testing for carrier couple parents.


Complete Gene Sequencing by Sanger Technology

 

 

 

 

 

 

 

 

 

 

Partner Reflex Sequencing

 

 

 

 

 

 

 

 

 

 

 

Other Molecular Testing

 

 



 

Insight offers complete gene sequencing by Sanger technology (coding exons +/- 30 bp of flanking intron) for the following, continually expanding list of genes/conditions:

  • ACADM - Medium chain acyl-CoA dehydrogenase deficiency
  • ACADS  – Short chain acyl-CoA dehydrogenase deficiency
  • ALDOB – Hereditary fructose intolerance
  • ASPA – Aspartoacylase deficiency/Canavan disease
  • CFTR – Cystic Fibrosis
  • CPT2 – Carnitine palmitoyltransferase II deficiency
  • DHCR7 – Smith-Lemli-Opitz syndrome
  • G6PC – Glycogen storage disease type 1a
  • GAA – Glycogen storage disease type II/Pompe disease
  • GBA – Gaucher Disease – Insight uses a combination of the long-range PCR and Sanger sequencing to assess the complete GBA gene while distinguishing it from a non-functioning but related pseudogene.
  • GJB2- GJB2-related DFNB1 nonsydromic hearing loss
  • HEXA – Tay-Sachs disease
  • MEFV – Familial Mediterranean fever
  • PMM2 – Hereditary disorder of glycosylation type 1a

 

Insight Medical Genetics offers rapid turnaround times for the reflex Sanger sequencing of the most commonly found recessive genes on many extended genotyping panels. Reflex sequencing is the best and most complete clinical strategy for assessing the risk of a couple giving birth to a child affected with the tested condition.  

Reflex sequencing should be performed on the spouse/partner of an individual who has already been determined to be a carrier of a mutation in one or more genes by prior genotype screening.  For example, if a woman who is currently pregnant or is planning to become pregnant is identified as a carrier by a genotyping panel, it is better to pursue full gene sequencing for the spouse or partner, which will yield a more complete assessment of his mutation status for that gene; reflexing to a genotyping panel would only test for the most common mutation, leaving considerable residual risk.

Insight will provide reflex sequencing within seven business days of specimen receipt for the above list of genes. As our capabilities continue to grow, please contact us for a complete list of genes.

Custom designed gene sequencing may also be developed on a case-by-case basis. Please contact us for details.

 

  • GJB2/GJB6 deletion testing – DFNB1 non-syndromic hearing loss
  • COL1A1/COL1A2 deletion testing – Osteogenesis Imperfecta
  • HBA1/HBA2 deletion testing – Alpha thalassemia
  • HBB Sanger Sequencing – Beta thalassemia, sickle cell disease, hemoglobin C disease, Hemoglobin E disease