Personalized Genomic Medicine

Columbia Custom Gene Panel (CCGP) testing is currently unavailable in the laboratory, as the list of offered panels is in the process of revision. Custom gene panels are still available after consultation with the laboratory. Please select from the revised list of genes when ordering. We anticipate reintroduction of panel testing shortly.

Genetics Testing

Genetic Testing is available in the Laboratory for Personalized Genomic Medicine. Click on the links below for a description of tests currently offered. For more information regarding genetic testing, email pgminquiry@cumc.columbia.edu.


Next Generation Sequencing

Columbia Custom Gene Panels

Purpose: Identify genetic basis of selected constitutional disorders (Click here for more details).  To assist with analysis of the proband’s genetic data, our policy is to test the parents or two other related individuals are processed together from the blood collection stage through the completion of the analysis.
Gene Selection for Testing: CLICK HERE for revised list of genes available for testing.
CPT Codes: 81479
Methodology: Agilent Sureselect capture and high throughput sequencing (Illumina MiSeq/HiSeq)
Turnaround Time: 90 days
Specimen: Anticoagulated blood in EDTA or Citrate, muscle biopsy, or high quality genomic DNA
Acceptance and Rejection Criteria: All specimens should carry two independent identifiers. Blood > 300 microliters, should be anti-coagulated, preferably with citrate or EDTA and should be less than a week old; muscle biopsy specimens (>50 mg) should be refrigerated from the time of biopsy to arrival to the lab; genomic DNA should be greater than 10kb median length. We optimally need 3 micrograms of genomic DNA at concentrations 50-200 ng/microliter. In addition, the standard acceptance and rejection criteria for specimens will apply.
Forms: 1. Requisition Form/Medical Questionnaire
2. CCGP Informed Consent (Adult)
3. CCGP Informed Consent (Children)
4. Medicare Advance Beneficiary Notice Form
5. Insurance Pre-Authorization Form

Whole Exome Sequencing (WES)

Purpose: Identify genetic basis of constitutional disorders (Click here for more details).  To assist with analysis of the proband’s genetic data, our policy is to test the parents or two other related individuals are processed together from the blood collection stage through the completion of the analysis.
CPT Codes: 81415, 81416(2), 81417(For reinterpretation only)
Methodology: Agilent Sureselect capture and high throughput sequencing (Illumina HiSeq)
Turnaround Time: 120 days
Samples Tested: Anticoagulated blood in EDTA or Citrate, muscle biopsy, or high quality genomic DNA
Acceptance and Rejection Criteria: All specimens should carry two independent identifiers. Blood > 300 microliters, should be anti-coagulated, preferably with citrate or EDTA and should be less than a week old; muscle biopsy specimens (>50 mg) should be refrigerated from the time of biopsy to arrival to the lab; genomic DNA should be greater than 10kb median length. We optimally need 3 micrograms of genomic DNA at concentrations 50-200 ng/microliter. In addition, the standard acceptance and rejection criteria for specimens will apply.
Associated documents: Mutations and disease associated genes that fall into the Agilent SureSelect Region of capture/interest (ROI): http://pathology.columbia.edu/diagnostic/PGM/xlsx/AgilentWESROI
The reportable range of WES is the genomic region that we guarantee reporting on. This corresponds to 95% of the Agilent ROI.
Predicted disease associated genes and mutations not guaranteed to be reported on ( within the Agilent Sureselect ROI, but outside the reportable range 5%) http://pathology.columbia.edu/diagnostic/PGM/xlsx/WESmutationsnotguaranteed
Incidental findings that are reported on: http://pathology.columbia.edu/diagnostic/PGM/pdf/reportableincidentals.pdf
Secondary Findings: ACMG Secondary Findings List
Forms: 1. Requisition Form/Medical Questionnaire
2. WES Informed Consent (Adults)
3. WES Informed Consent (Children)
3. Medicare Advance Beneficiary Notice Form
4. Insurance Pre-Authorization Form


Chromosomal Microarray

SNP Oligonucleotide Microarray Analysis (SOMA)

Purpose: Identify copy number changes associated with disease.
CPT Codes: 81229
Methodology: Whole genome SNP based cytogenomic microarray analysis. For prenatal specimens, we also offer a targeted approach whereby we report clinically significant copy number changes in our “Prenatal Custom" regions.
Turnaround Time: 7 days for prenatal specimens
14 days for non-prenatal specimens
Specimen: Peripheral blood, amniotic fluid (direct or cultured), chorionic villus sample (direct or cultured), products of conception (direct or cultured), DNA (extracted in a CLIA facility)
Forms: 1. Requisition Form/Medical Questionnaire
2. Informed Consent Form - SOMA
3. Insurance Pre-Authorization Form


Molecular Genetic Testing

C9orf GGGGCC Repeat Expansion

Purpose: To detect expansion of Hexonucleotide repeat causing Amyotrophic Lateral Sclerosis (ALS) and FTP.
CPT Codes:  
Methodology: Capillary Electrophoresis
Turnaround Time: 14 days
Specimen: Blood
Forms:  

Cystic Fibrosis Screening

Purpose: Reproductive carrier screening for common CFTR mutations 23 and 60.
CPT Codes: 81220
Methodology: Multiplexed PCR with bead hybridization
Turnaround Time: 14 days
Specimen: Blood in EDTA
Forms: 1. Requisition Form/Medical Questionnaire
2. Informed Consent Form - Cystic Fibrosis Screening

FMR1 by PCR with Reflex to Southern Blotting

Purpose: Detect CGG repeat expansions in the 5' untranslated region (5'UTR) of the FMRI1 gene to:
1. Diagnose or exclude Fragile X Syndrome, in children developmental delay;
2. Support a diagnosis of Fragile X Tremor Ataxia Syndrome (FXTAS) in adults;
3. Aid in the diagnosis of women with early menopause or premature ovarian failure.  
4. Detect female carriers (reproductive carrier screening).
CPT Codes: 81243
Methodology: Separate PCR reactions, one with flanking primers for sizing of alleles up to approximately 100 CGG repeats;  and the other, a “repeat-primed PCR” that will amplify most if not all larger alleles. Reflex to Southern Blotting with methylation sensitive restriction enzymes to distinguish between large premutations and full mutations.
Reference Range: NORMAL ALLELE: 5-40 repeats; MUTABLE NORMAL ALLELE: 41-54 repeats;
PREMUTATION ALLLE: 55-approximately 200 repeats; FULL MUTATION ALLELE: Greater than 200 repeats (usually fully methylated)
Turnaround Time: 14 days
Specimen: Blood in EDTA
Forms: 1. Requisition Form/Medical Questionnaire
2. Informed Consent Form - FMR1 Fragile X

LGI1Test

Purpose: To detect mutations in the LGI1 gene.
CPT Codes: 81479
Methodology: Sanger Sequencing
Turnaround Time: 14 days
Specimen: Blood in EDTA
Forms: Requisition Form/Medical Questionnaire

Prader-Willi / Angelman Syndrome DNA Analysis

Purpose: To detect abnormal parent-specific imprinting within the Prader-Willi critical region (PWCR) on 15q11-13.
CPT Codes: 81331
Methodology: Southern Blotting
Turnaround Time: 21 days
Ssamples tested: Blood in EDTA
Forms: 1. Requisition Form/Medical Questionnaire
2. Informed Consent Form - Prader-Willi Angelman Syndrome

Sanger Sequencing of Individual Variance

Purpose: To determine inheritance patterns and possible pathogenicity of variants found by array or NGS platform-based testing.
CPT Codes: 81479
Methodology: Sanger Sequencing
Turnaround Time: 30 days
Specimen: Blood in EDTA
Forms: Requisition Form/Medical Questionnaire

Thrombophilia Risk Panel 1

Purpose: To detect common variants in Factor II (prothrombin) and Factor V which serve as genetic risk factors to thrombosis.
CPT Codes: 81240, 81241, 81291
Methodology: GenMark eSensor System
Turnaround Time: 14 days
Specimen: Blood in EDTA
Forms: 1. Requisition Form/Medical Questionnaire
2. Informed Consent Form - Thrombophilia Risk Panel

Thrombophilia Risk Panel 2

Purpose: To detect common variants in Factor II (prothrombin), Factor V and MTHFR which serve as genetic risk factors to thrombosis.
CPT Codes: 81240, 81241
Methodology: GenMark eSensor System
Turnaround Time: 14 days
Specimen: Blood in EDTA
Forms: 1. Requisition Form/Medical Questionnaire
2. Informed Consent Form - Thrombophilia Risk Panel

Warfarin Sensitivity Test

Purpose: To detect variants associated with variable response to Warfarin therapy.
CPT Codes: 81227
Methodology: GenMark eSensor System
Turnaround Time: 7 days
Specimen: Blood in EDTA
Forms: Requisition Form/Medical Questionnaire


 
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