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HelpTest Code LAB2921 Cholestasis Genetic Panel
Clinical System Name
Cholestasis Genetic Panel
Description
This is a Next-Gen sequencing panel with CNV detection that includes 77 genes:
ABCB11, ABCB4, ABCC2, ABCG5, ABCG8, ACOX2, AKR1C4, AKR1D1, ALDOB, AMACR, ATP8B1,
BAAT, CC2D2A, CFTR, CLDN1, CYP27A1, CYP7A1, CYP7B1, DCDC2, DGUOK, DHCR7, EHHADH,
FAH, GNAS, GPBAR1, HNF1B, HSD17B4, HSD3B7, INVS, JAG1, KMT2D, LIPA, MKS1, MPV17, M
YO5B, NOTCH2, NPC1, NPC2, NPHP1, NPHP3, NPHP4, NR1H4, PEX1, PEX10, PEX11B, PEX12,
PEX13, PEX14, PEX16, PEX19, PEX2, PEX26, PEX3, PEX5, PEX6, PEX7, PKD1L1, PKHD1, POLG,
SCP2, SERPINA1, SLC10A1, SLC10A2, SLC25A13, SLC27A5, SLC51A, SLC51B, SLCO1B3,
SMPD1, TALDO1, TJP2, TMEM216, TRMU, UGT1A1, UTP4, VIPAS39, VPS33B. Please contact the Seattle Children's Laboratory genetic counselors with questions (LabGC@seattlechildrens.org)
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
Reference Range
Interpretive report provided.
Methodology
This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.
This panel typically provides 99% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing.
Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).
Special Instructions
Clinical Utility
Neonatal cholestasis is often clinically defined as the prolonged occurrence of conjugated hyperbilirubinemia in the newborn period, due to impairments in the flow of bile. It is caused by a diverse group of hepatobiliary diseases with overlapping clinical presentations, supporting a need for a multi-gene diagnostic panel.
The incidence of neonatal cholestasis is estimated to be 1 in 2500 live births. Genetic and metabolic causes account for at least 25% to 30% of all cases of neonatal cholestasis, generally due to impairments of hepatobiliary transport, intermediary metabolism, storage disorders, or bile duct dysgenesis. Several of these disorders are life-threatening and benefit from early diagnosis and intervention, yet diagnosing the specific cause via routine serum chemistries or by evaluation of liver biopsies is not as definitive as direct genetic testing.Moreover, several cholestatic entities develop in adults that are caused by variants in these same genes.
Send Out Instructions
| Reference Test Name: | Cholestasis NextGen sequencing and CNV Panel |
| Reference Test Number: | 13371 - SP144 |
| Instructions: |
Ship whole blood overnight, ambient temperature. PreventionGenetics accepts Saturday delivery |