Test Code LAB2921 Cholestasis Genetic Panel
Clinical System Name
Cholestasis Genetic Panel
Description
No-charge genetic testing for qualifying U.S.-resident patients through a program sponsored by Mirum Pharmaceuticals. Panel analyzing 143 genes associated with cholestasis: ABCB11, ABCB4, ABCC12, ABCC2, ABCD3, ABCG5, ABCG8, ACBD5, ACOX1, ACOX2, ADK, AHI1, AKR1C4, AKR1D1, ALDOA, ALDOB, ALMS1, AMACR, ANKS6, AP1S1, ARL13B, ATP7B, ATP8B1, B9D1, B9D2, BAAT, BBS1, BBS10, BBS12, BBS2, BBS4, BCS1L, BLVRA, CC2D2A, CEP290, CFTR, CLDN1, COG6, COG7, CYP27A1, CYP7A1, CYP7B1, DCDC2, DGUOK, DHCR7, EHHADH, EPHX1, FAH, GALE, GALT, GFM1, GLIS3, GNAS, HADHA, HNF1B, HSD17B4, HSD3B7, IFT56, IFT81, IFT88, INVS, IQCB1, JAG1, KIF12, KMT2D, LIPA, LSR, MKKS, MKS1, MPI, MPV17, MVK, MYO5B, NBAS, NEK8, NOTCH2, NPC1, NPC2, NPHP1, NPHP3, NPHP4, NR1H4, OFD1, PEX1, PEX10, PEX11B, PEX12, PEX13, PEX14, PEX16, PEX19, PEX2, PEX26, PEX3, PEX5, PEX6, PKD1, PKD1L1, PKD2, PKHD1, PLEC, POLG, PPM1F, PSKH1, RAB11A, RFX6, RINT1, RPGRIP1L, SC5D, SCP2, SCYL1, SEMA7A, SERPINA1, SLC10A1, SLC10A2, SLC25A13, SLC27A5, SLC37A4, SLC51A, SLC51B, SLCO1B3, SMPD1, STX3, STXBP2, TALDO1, TCTN3, TJP2, TMEM216, TMEM67, TRIM37, TRMU, TULP3, UGT1A1, UNC45A, USP53, UTP4, VIPAS39, VMA22, VPS33B, WDR83OS, YARS1, ZFYVE19, ZNF423
Sample Requirements
Specimen: Whole Blood
Container(s): Lavender Top/EDTA, Yellow/ACD
Preferred Vol: 5 mL
Minimum Vol: 3 mL (1 mL for small infants)
Specimen: DNA
Container(s): Sterile plastic tube
Preferred Vol: 10 µg of purified DNA at a concentration of at least 100 ng/μL
Minimum Vol: 5 µg of purified DNA at a concentration of at least 100 ng/μL
Alternative Specimen (e.g. salvia or buccal): Alternate Specimen Collection Kits for Genetic Testing
Processing Instructions
Reject due to:
Spin: N
Aliquot: N
Temp: 2 - 4 C
Storage location: Do not spin. Deliver blood to the Send Outs refrigerator rack.
Off-site collection:
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole blood | Room temp | 3 d |
| Whole blood | Refrigerated | 7 d |
| Whole blood | Frozen | N |
| Extracted DNA | Room temp | 3-4 d |
| Extracted DNA | Refrigerated | 1 y |
| Extracted DNA | Frozen | Indefinitely |
Availability
| STAT | Performed | TAT |
|---|---|---|
| N | Drawn daily | 3-4 w |
Performing Laboratory
PreventionGenetics
3800 South Business Park Avenue
Marshfield, WI 54449
Phone Number: (715) 387-0484
Department
Department: Send Outs/Genetic
Phone: (206) 987-2563
Methodology
Next-generation sequencing with orthogonal methods (i.e., Sanger sequencing, array) as needed.
Reference Range
Interpretive report provided.
Special Instructions
Send Out Instructions
| Reference Test Name: | Cholestasis Sponsored Testing Program |
| Reference Test Number: | 16229 |
| Instructions: |
Ship whole blood overnight, ambient temperature. PreventionGenetics accepts Saturday delivery |
Clinical Utility
Hereditary cholestatic liver disease is a heterogenous group of disorders with complex pathophysiology, often presenting with overlapping symptoms such as jaundice, pruritus, failure to thrive, hepatomegaly, and other liver abnormalities. At the molecular level, cholestasis is caused by a reduction of bile flow due to impaired hepatocyte secretion or obstruction of bile ducts as a result of defective hepatocyte transport, disorders of bile duct development, inborn errors of bile acid metabolism, and other metabolic disorders impacting the liver. Hereditary cholestasis often, but not always, presents in the neonatal period, and may present with extrahepatic manifestations as well as systemic disease. The estimated worldwide incidence of cholestasis ranges considerably depending on population. Pediatric cholestasis is estimated to affect about 1:2500 in newborns, while intrahepatic cholestasis of pregnancy is estimated to affect between ~0.1-5.2% of pregnancies worldwide, with up to ~9-25% of pregnancies affected in some South American populations. The prevalence of cholestasis among patients with inflammatory bowel disease is as high as 7%. Some hereditary forms of cholestatic liver disease are known to occur more frequently in ethnic groups where consanguineous marriage is prevalent or in some geographic regions due to founder effects.
Advantages of genetic testing for cholestasis include confirmation of diagnosis, identification of other health risks associated with syndromic disease, optimization of therapeutic management, allowing for targeted testing of other family members, and assistance with reproductive planning. This test especially aids in a differential diagnosis of similar phenotypes by analyzing multiple genes simultaneously that all include the clinical feature of cholestasis.