Molecular Diagnostics Nucleic Acid Isolation

The Molecular Diagnostics section of the BMP Core Shared Resource offers nucleic acid isolation from a variety of different specimen types including blood, fresh or frozen tissue, and FFPE (including micro-dissection). Included in the price of each extraction is nucleic acid quantification by NanoDrop andgeneration of a nucleic acid isolation report. Additional fees apply for Biorepository and Research Histology Services and quantification by Qubit and Agilent TapeStation RIN analysis.

Human Specimens from the Biorepository under the General BioBanking and Using IRB Protocol

If requesting human specimens from the Biorepository through the general biobanking and using IRB protocol, please make a request to BMP-Biorepository@hci.utah.edu. The Biorepository staff will coordinate consent validation, specimen collection or retrieval, histology, and neoplastic cell content review by a pathologist and will deliver the specimens to the Molecular Diagnostics Laboratory for extraction. A GNomEx request for the nucleic acid isolation will be made on behalf of the investigator, and the sample will be de-identified and assigned a Specimen ID number in LabVantage. Upon completion, the investigator will be notified, and the nucleic acid isolation report will be available through GNomEx.

De-identified (exempt) Human and Animal Specimens

Please submit a GNomEx request directly to the Molecular Diagnostics Laboratory for de-identified (exempt) human and animal specimens. Please see the sample submission page for additional instructions.

Isolation Services

DNA from blood, buffy coat, plasma or serum (Qiagen QIAamp DNA Blood Mini Kit Cat# 51185)

• Input: Up to 0.2 mL of fresh and frozen whole blood with common anticoagulants, such as EDTA, citrate, or heparin and buffy coat, PBMC, plasma or serum.
• Extraction Notes: Elution in 100 µL of buffer AE (10 mM Tris-HCl, 0.5 mM EDTA pH 9.0)

cfDNA from plasman (Qiagen QIAamp Circulating Nucleic Acid Kit Cat #55114)

• Input: 5 to 10 mL plasma or CSF (whole blood collected in Streck Cell-Free DNA 10 mL BCT tubes (or equivalent) )
• Extraction Notes: Elution in 42 µL IDTE

DNA and RNA from fresh or frozen tissue (Qiagen AllPrep DNA/RNA/miRNA Universal Kit Cat# 80224)

• Input: 30 mg of fresh or frozen tissue
• Extraction Notes: RNA is eluted in 60 µL RNase-free water. and DNA is eluted in 100 µL of buffer EB (10 mM Tris-HCl pH 8.5).

DNA FFPE (Qiagen QiaAMP DNA FFPE Kit Cat# 56404)

• Micro-Dissection Input: Circled H&E and up to 8 sections at 10 microns thick, unstained or aniline blue slides with tissue area of 250 mm2 or 15-20 sections for smaller specimens and biopsies
• Scrolls and Punches Input: Two to 5 scrolls at 10 microns thick. Punches larger than 2-3 mm are challenging to digest.
• Extraction Details:  Elution in 40 µL of buffer ATE (10 mM Tris-HCl, 0.1 mM EDTA, 0.04% Sodium Azide pH 8.3)

RNA FFPE (Qiagen miRNeasy FFPE Kit Cat# 73504) OR (Qiagen miRNeasy FFPE Kit Cat# 217504)

• Micro-Dissection Input: Circled H&E and Up to 8 sections at 10 microns thick, unstained or ainline blue slides with tissue area of 250 mm2 or 15-20 sections for smaller specimens and biopsies
• Scrolls and Punches Input: Two to 5 scrolls at 10 microns thick. Punches larger than 2-3 mm are challenging to digest.
• Extraction Notes: DNase digestion performed prior to elution in 20 µL RNase-free water. Extracted RNA samples for RNAseq will have a second Dnase I treatment.

Purigen System

DNA from FFPE (bionano Ionic G2 FFPE to DNA kit Cat# 33006)

• Input: One 10 um section of FFPE tissue (scroll or side-mounted) with an area of 50-300 mm2
• Extraction Notes: ~50  µL of DNA extracts collecte

RNA from FFPE (bionano Ionic G2 FFPE to DNA kit Cat# 33010)

• Input: One 10 um section of FFPE tissue (scroll or side-mounted) with an area of 50-300 mm2
• Extraction Notes: ~50  µL of DNA extracts collected

FFPE Micro-Dissection

The Molecular Diagnostics laboratory strongly recommends micro-dissection of FFPE specimens to enrich for tumor cells. Many FFPE specimens contain only small amounts of tumor, which can significantly impact downstream results. We highly recommend you collaborate with a pathologist to circle the tumor area on the H&E. Visit our FAQ page to learn more about finding a pathologist.

Turnaround Time and Low Volume Requests

Isolations will be performed in the order they were received. The typical turnaround time is approximately 2 weeks after the Molecular Diagnostics laboratory has physically received the specimens, but may be as long as 4-6 weeks. If a request is submitted for fewer than 4 specimens, we will wait up to one month for additional samples to be requested. Alternatively, the investigator can pay for 4 samples, and the extraction will be processed in the order it was received.