Genomic Medicine

Genomic Medicine

SR NOTESTTEST COMPONENTSMETHODSPECIMEN/ TRANSPORTTATCLINICAL APPLICATIONS
1Donor Specific Antigen (DSA) (Luminex)Antigen-Antibody reaction is determined (positive or negative).Luminex solid phase assayDonor: Sodium Heparin Vacutainer (3ml x 5 vials); Recipient: Plain Vacutainer (3ml x 2 vials)3 daysThis test is ordered after a potential donor has been identified. It helps to determine if the recipient has specific antibodies against antigens present on the donor's lymphocytes. Serum from the recipient is mixed with white blood cells (T and B lymphocytes) of the donor. If any reaction has been detected (a positive result) that would indicate the incompatibility between two of them. The cross match result should be always interpreted along with the known information about the recipient's HLA antibodies and the donor's HLA typing.
2LCM-CDCAntigen-Antibody reaction in the format of percentageManualDonor: Sodium Heparin Vacutainer (3ml x 5 vials); Recipient: Plain Vacutainer (3ml x 2 vials)3 daysThis test is ordered after a potential donor has been identified. It helps to determine if the recipient has specific antibodies against antigens present on the donor's lymphocytes. Serum from the recipient is mixed with white blood cells (T and B lymphocytes) of the donor. If any reaction has been detected (a positive result) that would indicate the incompatibility between two of them. The cross match result should be always interpreted along with the known information about the recipient's HLA antibodies and the Donor’s HLA Typing
3HLA ABCDRDQ Low resolutionHLA-ABCDRDQ alelles in low resolutionSSO PCR method by LuminexEDTA whole blood (3ml), Buccal Swab3 daysTo Determine HLA compatibility between specimens from bone marrow and solid organ transplant candidates and their donors
4SINGLE ANTIGEN CLASS I AND IInegative or positive antibody detection of HLA Class I & IILuminex solid phase assayRecipient: Plain Vacutainer (3ml x 2 vials)4 daysThis assay is used for the detection of pre & post transplantation HLA antibodies in solid organ transplant recipients and in unmatched Bone marrow transplants. It detects antibodies against HLA Class I antigens.
5Antibody Screening for HLA Class I and II (PRA)negative or positive antibody detection of HLA Class I, Class II and MIC antibodyLuminex solid phase assayRecipient: Plain Vacutainer (3ml x 2 vials)4 daysThis assay is used for the detection of pre & post transplantation HLA antibodies in solid organ transplant recipients and in unmatched Bone marrow transplants.
6BK Polyoma Virus Quantitative DetectionQualitative detection of BK polyomavirusReal Time PCREDTA whole blood (3ml), Urine, CSF1 dayDouble-stranded DNA virus
Human polyomavirus (genetically similar to JC virus)
BK virus becomes latent in the kidneys and urinary tract after primary infection
Reactivated BK virus infection may occur with immunosuppression
7JC Polyoma Virus Quantitative DetectionQualitative detection of JC polyoma virusReal Time PCREDTA whole blood (3ml), Urine, CSF1 dayJC virus (JCV), a member of the genus Polyomavirus, is a small nonenveloped DNA-containing virus. Primary infection occurs in early childhood, with a prevalence of greater than 80%. The virus is latent but can reactivate in immunosuppressed patients
8CMV (Cytomegalovirus) DNA Qualitative DetectionQualitative detection of Human Cytomegalovirus (CMV)Real Time PCREDTA whole blood (3ml)1 dayLargest member of the herpesvirus family; double-stranded DNA virus
Ability to remain latent (feature of all herpes viruses)
Large intranuclear and cytoplasmic inclusions produced in tissues by CMV are the hallmark of the disease
9CMV (Cytomegalovirus) DNA Quantitative AnalysisQuantitative detection of Human Cytomegalovirus (CMV)Real Time PCRCSF, EDTA whole blood (3ml)1 dayLargest member of the herpesvirus family; double-stranded DNA virus
Ability to remain latent (feature of all herpes viruses)
Large intranuclear and cytoplasmic inclusions produced in tissues by CMV are the hallmark of the disease
10Clinical exome sequencing.A panel of genes.NGSPreferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration. Specimen at room temperature. Also acceptable: Refrigerated. Ship in cooled container during summer months.20Clinical exome sequencing (CES) is rapidly becoming a common molecular
diagnostic test for establishing a definitive molecular diagnosis of individuals with rare genetic disorders which can allow for:
-Better understanding of the natural history/prognosis
-Targeted management (anticipatory guidance, management changes, specific therapies)
-Predictive testing of at-risk family members
-Testing and exclusion of disease in siblings or other relatives
-Recurrence risk assessment
-Reproductive decision-making
Serving as a second-tier test for patients in whom previous genetic testing for specific syndromes was negative
Providing a potentially cost-effective alternative to establishing a molecular diagnosis compared to multiple independent molecular assays
11Maple Syrup Urine Disease PanelDBT, DLD, BCKDHA, BCKDHB genesNext-Generation SequencingPreferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration20 daysThis test is used to screen for mutations in the genes responsible for MSUDP. This test helps in determining the necessity for screening in other family members. In cases of a positive finding in a patient of child bearing age, Preimplantation genetic diagnosis can be performed in most cases to help conceive a child without the pathogenic mutation.
12Urea Cycle Disorders PanelPanel of genes- ACADM, ACADS, ACADVL, ARG1, ASL, ASS1, BCKDHA, BCKDHB,
CPS1, CPT1A, CPT2, DBT, DLD, ETFA, ETFB, ETFDH, GLUD1, HADHA, HADHB, HCFC1,
HLCS, HMGCL, HMGCS2, IVD, MCCC1, MCCC2, MMAA, MMAB, MMACHC, MMADHC
(C2ORF25) , MUT, NAGS, OTC, PC, PCCA, PCCB, SLC22A5, SLC25A13, SLC25A15,
SLC25A20, SLC7A7, SUCLA2, SUCLG1, TMEM70
Next-Generation SequencingPreferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration20 daysMolecular confirmation of a clinical diagnosis
Testing of patients suspected of having a urea cycle disorder, transporter defect or unexplained hyperammonemia
Prenatal diagnosis for known familial mutation(s) in at-risk pregnancies
13Polycystic Kidney DiseaseAutosomal Dominant Polycystic Kidney Disease - PKD1 and PKD2 genes
Autosomal Recessive Polycystic Kidney Disease - PKHD1
Next-Generation SequencingPreferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration20 daysThis test is used to screen for mutations in the genes responsible for PKD. This test helps in determining the necessity for screening in other family members. In cases of a positive finding in a patient of child bearing age, Preimplantation genetic diagnosis can be performed in most cases to help conceive a child without the pathogenic mutation.
14Primary Hyperoxaluria types 1 & 2AGXT, GRHPR and HOGA1 GenesNext Generation SequencingEDTA whole blood (3ml)20 DaysThis test is used to screen for the mutations in the AGXT and GRHPR gene responsible for Primary Hyperoxuluria types 1 & 2. Detection of pathogenic mutation in an individual can lead to a diagnosis, possible prognosis, and prospective therapy treatments.
15Renal Hypouricemia (SLC22A12 & SLC2A9)SLC22A12 and SLC2A9 GeneSanger SequencingWhole blood 3ml in EDTA vacutainer20 daysDetection of pathogenic mutation in an individual can lead to a diagnosis, possible prognosis, and prospective therapy treatments.
16Tacrolimus Mutation StudyTargeted Mutation in CYP3A4Sanger SequencingWhole blood 3ml in EDTA vacutainer7 DaysTacrolimus is a macrolide antibiotic derived from the fungus Streptomyces tsukubaensis. Like cyclosporine, tacrolimus inhibits calcineurin to suppress T cells. Tacrolimus is metabolized by CYP3A4, thus its concentrations are affected by drugs that inhibit (calcium channel blockers, antifungal agents, some antibiotics, grapefruit juice) or induce (anticonvulsants, rifampin) this enzyme. Tacrolimus has a narrow therapeutic range, and adverse effects are common, particularly at high dose and concentrations, making therapeutic drug monitoring essential