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 is detected (a positive result), it 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 is detected (a positive result), it 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 alellesSSO 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
4HLA ABCDRDQ HIGH RESOLUTIONHLA-ABCDRDQ alellesSBT methodEDTA whole blood (3ml), Buccal Swab7 daysTo Determine HLA compatibility between specimens from bone marrow and solid organ transplant candidates and their donors
5SINGLE 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.
6Antibody 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.
7Clinical exome sequencingA panel of genesNGSPreferred 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
8Urea 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
9Polycystic 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.
10Alport Syndrome (COL4A5)Coding region along with certain intronic padding of COL4A3, COL4A4 and COL4A5 genes associated with Alport Syndrome.Next-Generation SequencingWhole blood 3ml in EDTA vacutainer20 daysThis test is used to screen for mutations in the genes responsible for ALPS. 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.
11Primary 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.
12Renal 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.
13Childhood onset Nephrotic syndromePanel of genes
ACTN4,COL4A5,LMX1B,SMARCAL1,ALG1,COQ2,MYH9,TRPC6,ALMS1,COQ6,MY01E,WT1,APOL1,COQ7,
NPHS1,ZMPSTE24,ARHGAP2,COQ9,NPHS2,ARHGDIA,CYP11B,PDSS2,CD151,INF2,PLCE1,CD2AP,ITGA3,
PMM2,COL4A3,ITGB4,PTPRO,COL4A4,
LAMB2,SCARB2
Next Generation SequencingEDTA whole blood (3ml)30 daysAid in diagnosis, especially a “fuzzy” phenotype such as FSGS with clinical features common to several forms of kidney injury; Help in determining risk of recurrent disease in kidney transplantation; Allowing for risk assessment in candidate living related kidney donors; Aid in prenatal diagnosis.
14Atypical Hemolytic Uremic SyndromeC3, CD46 (MCP), CFB, CFH, CFHR1, CFHR3, CFHR4, CFI, DGKE, and THBDNext Generation SequencingWhole blood 3ml in EDTA vacutainer30 daysHemolytic-uremic syndrome (HUS) is characterized by hemolytic anemia, thrombocytopenia, and renal failure caused by platelet thrombi in the microcirculation of the kidney and other organs. The onset of atypical HUS (aHUS) ranges from the neonatal period to adulthood. 
15CMV (Cytomegalo Virus) DNA Qualitative DetectionQualitative detection of Human Cytomegalovirus (CMV)Real time Polymerase Chain ReactionWhole blood 3ml in EDTA vacutainer Urine, Plasma, CSF, Body fluids1 dayCMV infection is of clinical significance primarily in pregnant women, newborn infants with possible congenital infection,
immunosuppressed transplant patients and immunocompromised individuals.
16CMV (Cytomegalo Virus) DNA Quantitative DetectionQuantitative detection of Human Cytomegalovirus (CMV)Real time Polymerase Chain ReactionWhole blood 3ml in EDTA vacutainer, Urine, Plasma, CSF, Body fluids1 dayCMV infection is of clinical significance primarily in pregnant women, newborn infants with possible congenital infection,
immunosuppressed transplant patients and immunocompromised individuals.
17BK Polyoma Virus Quantitative DetectionQuantitative detection of BK polyoma virusReal time Polymerase Chain ReactionWhole blood 3ml in EDTA vacutainer, Urine, Plasma1 dayThe presence of BKV DNA in blood reflects the dynamics of the disease: the conversion of plasma from negative to positive for BKV DNA after transplantation, the presence of DNA in plasma in conjunction with the persistence of nephropathy, and its disappearance from plasma after the reduction of immunosuppressive therapy. However, BKV DNA is typically detectable in urine prior to plasma and may serve as an indication of impending BKV associated nephropathy.
18Adenovirus Qualitative DetectionQualitative detection of AdenovirusReal time Polymerase Chain ReactionWhole blood 3ml in EDTA vacutainer, Urine, Plasma, CSF, Body fluids1 dayThe rapid detection and quantitation of adenovirus DNA by a sensitive PCR technique will aid in the diagnosis and treatment monitoring of adenovirus infections, particularly in immunocompromised patients.