Fixation Effects on Variant Calling in a Clinical Resequencing Panel
Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alterna...
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| Published in: | The Journal of molecular diagnostics : JMD Vol. 21; no. 4; pp. 705 - 717 |
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| Main Authors: | , , , , , , , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
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Elsevier Inc
01-07-2019
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| Abstract | Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review. |
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| AbstractList | Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review. |
| Author | Starks, Elizabeth Docking, T. Roderick Filipenko, Douglas Phang, P. Terry Raval, Manoj Zhou, Chen Yap, Shyong Quin Xiong, Wei Parker, Jeremy D.K. Brown, Carl J. Swanson, Lucas Slind, Jillian Fuller, Megan Karsan, Aly Walker, Blair Karimuddin, Ahmer A. |
| Author_xml | – sequence: 1 givenname: Jeremy D.K. orcidid: 0000-0001-8319-5891 surname: Parker fullname: Parker, Jeremy D.K. organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada – sequence: 2 givenname: Shyong Quin surname: Yap fullname: Yap, Shyong Quin organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada – sequence: 3 givenname: Elizabeth surname: Starks fullname: Starks, Elizabeth organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada – sequence: 4 givenname: Jillian surname: Slind fullname: Slind, Jillian organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada – sequence: 5 givenname: Lucas orcidid: 0000-0002-7074-4991 surname: Swanson fullname: Swanson, Lucas organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada – sequence: 6 givenname: T. Roderick orcidid: 0000-0003-3248-4081 surname: Docking fullname: Docking, T. Roderick organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada – sequence: 7 givenname: Megan surname: Fuller fullname: Fuller, Megan organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada – sequence: 8 givenname: Chen surname: Zhou fullname: Zhou, Chen organization: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 9 givenname: Blair surname: Walker fullname: Walker, Blair organization: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 10 givenname: Douglas surname: Filipenko fullname: Filipenko, Douglas organization: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 11 givenname: Wei orcidid: 0000-0002-2932-6886 surname: Xiong fullname: Xiong, Wei organization: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 12 givenname: Ahmer A. surname: Karimuddin fullname: Karimuddin, Ahmer A. organization: Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 13 givenname: P. Terry surname: Phang fullname: Phang, P. Terry organization: Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 14 givenname: Manoj surname: Raval fullname: Raval, Manoj organization: Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 15 givenname: Carl J. orcidid: 0000-0002-5368-3541 surname: Brown fullname: Brown, Carl J. organization: Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada – sequence: 16 givenname: Aly surname: Karsan fullname: Karsan, Aly email: akarsan@bcgsc.ca organization: Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada |
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| CitedBy_id | crossref_primary_10_3389_fgene_2024_1420190 crossref_primary_10_1016_j_acthis_2022_151880 crossref_primary_10_1016_j_watres_2021_117696 crossref_primary_10_1007_s00428_023_03692_6 |
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| Title | Fixation Effects on Variant Calling in a Clinical Resequencing Panel |
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