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Test Code LAB2921 Cholestasis Genetic Panel

Important Note

A completed Cholestasis Panel test requisition form is required to proceed with this testing.

Please email completed paperwork to ReferenceLabTeam@seattlechildrens.org (NOTE - Please do not give family paperwork to family to drop off in lab).

 

Contact the LabGC team to discuss testing and/or obtain a copy of the required forms. LabGC@seattlechildrens.org

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

Prevention Genetics

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.