{"id":823,"date":"2023-07-21T11:33:31","date_gmt":"2023-07-21T18:33:31","guid":{"rendered":"https:\/\/depts.washington.edu\/cfar\/wordpress\/?page_id=823"},"modified":"2025-06-18T13:13:50","modified_gmt":"2025-06-18T20:13:50","slug":"biomarkers-prevention-and-interventions-for-hiv-associated-malignancies-and-ncds-core","status":"publish","type":"page","link":"https:\/\/depts.washington.edu\/cfar\/cores\/biomarkers-prevention-and-interventions-for-hiv-associated-malignancies-and-ncds-core\/","title":{"rendered":"Biomarkers, Prevention and Interventions for HIV-associated Malignancies and NCDs Core"},"content":{"rendered":"<p class=\"intro\">The Biomarkers, Prevention and Interventions for HIV-associated Malignancies and NCDs (BPIN) Core provides assays and data instruments to enable studies of HIV-associated malignancies.<\/p>\n<p>Cancer has become the leading cause of death among persons with HIV infection worldwide. Kaposi sarcoma, non-Hodgkin lymphoma, and cervical cancer were recognized as AIDS-Defining Malignancies (<strong>ADM<\/strong>) early in the epidemic. In the setting of broadly available ART, cancer now impacts persons living with HIV both at the time of diagnosis and as a consequence of long-term HIV infection. In addition to ADM, people living with HIV are at increased risk of a range of cancers, including lung cancer, anal cancer, Hodgkin lymphoma, liver cancer, and head and neck cancer. Importantly, comorbid HIV infection is associated with more than a two-fold increased risk of death among persons with cancer compared with persons of the same age, sex, and stage of cancer without HIV infection. Despite more than three decades of recognizing an association between HIV and cancer, significant differences remain in our knowledge about the etiology, natural history and treatment of HIV-associated malignancies (<strong>HIVAM<\/strong>). Immunotherapeutic approaches to treating cancer in the setting of HIV are emerging as important options. To address unanswered question in the field of HIV and cancer, we are proactively continuing to foster and strengthen research in our local and global HIV communities through these specific aims:<\/p>\n<ol>\n<li>Support design and implementation of studies addressing the <strong>changing epidemiology<\/strong> of HIVAM <strong>across the globe<\/strong><\/li>\n<li>Foster <strong>development and evaluation of new technologies for the treatment and prevention<\/strong> of HIVAM through rigorous pre-clinical, translational and early-clinical studies<\/li>\n<li><strong>Promote state-of-the-art technology for the pathologic and molecular diagnosis and monitoring<\/strong> of HIVAM<\/li>\n<\/ol>\n<div class=\"tab-tour  vertical-tour\" id=\"tabs-tour-container\">\n<div class=\"screen-reader-text\"><\/div>\n<div class=\"row\">\n<div class=\"col-3\">\n<ul class=\"nav flex-column nav-pills\" id=\"tab-tour\" role=\"tablist\" aria-orientation=\"vertical\">\n<li class=\"nav-item\" role=\"presentation\"><button role=\"tab\" class=\"nav-link active\" type=\"button\" id=\"title-tab-tour-1\" data-toggle=\"tab\" href=\"#tab-tour-1\"  aria-controls=\"tab-tour-1\" aria-selected=\"true\" >Services<\/button><\/li>\n<li class=\"nav-item\" role=\"presentation\"><button role=\"tab\" class=\"nav-link\" type=\"button\" id=\"title-tab-tour-2\" data-toggle=\"tab\" href=\"#tab-tour-2\"  aria-controls=\"tab-tour-2\" aria-selected=\"false\" tabindex=\"-1\">Activities<\/button><\/li>\n<li class=\"nav-item\" role=\"presentation\"><button role=\"tab\" class=\"nav-link\" type=\"button\" id=\"title-tab-tour-3\" data-toggle=\"tab\" href=\"#tab-tour-3\"  aria-controls=\"tab-tour-3\" aria-selected=\"false\" tabindex=\"-1\">People<\/button><\/li>\n<li class=\"nav-item\" role=\"presentation\"><button role=\"tab\" class=\"nav-link\" type=\"button\" id=\"title-tab-tour-4\" data-toggle=\"tab\" href=\"#tab-tour-4\"  aria-controls=\"tab-tour-4\" aria-selected=\"false\" tabindex=\"-1\">Contact<\/button><\/li>\n<\/ul>\n<\/div>\n<div class=\"col-9\">\n<div class=\"tab-content\" id=\"tab-content-tab-tour\">\n<div class=\"tab-pane fade show active\" id=\"tab-tour-1\" role=\"tabpanel\" aria-labelledby=\"title-tab-tour-1\" tabindex=\"0\">\n<div class=\"content_block\" id=\"custom_post_widget-829\">\n<div class=\"su-spoiler su-spoiler-style-default su-spoiler-icon-caret su-spoiler-closed\" data-scroll-offset=\"0\" data-anchor-in-url=\"no\">\n<div class=\"su-spoiler-title\" role=\"button\"><span class=\"su-spoiler-icon\"><\/span>HIVAM Laboratory and Biorepositories (HCRI-Uganda)<\/div>\n<div class=\"su-spoiler-content su-u-clearfix su-u-trim\">\nThe Uganda Cancer Institute Fred Hutchinson Cancer Research Center Facility has an 8,000<br \/>\nft 2 laboratory with facilities that can support IRB approved HIVAM research. The laboratory has<br \/>\nspecimen processing and storage, histopathology, BSL2\/3 studies, and a steadily expanding<br \/>\ncapability for molecular analysis that includes standard real-time PCR and a 16-channel<br \/>\nGeneXpert as well as high throughput sequencing on the Illumina MiSeq platform. The<br \/>\nlaboratories are supported by 6 full-time lab technicians and data staff and are overseen by an<br \/>\nActing Laboratory Director.<\/p>\n<p>The laboratory also has a dedicated 337 sq. foot climate and access controlled biospecimen<br \/>\nrepository that supports HIVAM research. The repository is setup to accommodate up to six -80-<br \/>\ndegree Fahrenheit freezers, one -20-degree Fahrenheit freezer, four ambient temperature<br \/>\nspecimen storage cabinets, and one Liquid Nitrogen (LN2) freezer with two LN2 supply tanks.<br \/>\nAll freezers are setup with a real-time temperature monitoring system that logs all temperature<br \/>\ndata and sends SMS to identified individuals in cases of temperatures occurring outside of<br \/>\nacceptable ranges.<\/p>\n<p>Storage of specimens is also available via refrigerator and freezer storage and is provided in<br \/>\nseparate, secured room in the laboratory; all refrigerators and freezers are supported by a back-<br \/>\nup generator and uninterruptible power supplies. Laboratory results and specimen storage data<br \/>\nare managed by a secure database (LIMS) system. The Laboratory staff have shipping<br \/>\nprotocols for the efficient transfer of specimens to North America on either dry ice or liquid<br \/>\nnitrogen and hold annual import permits for the US CDC, the National Drug Authority of Uganda<br \/>\nand additional international permits as needed. Office space for the lab supervisor and auxiliary<br \/>\nstaff contains six computer stations, printers, fax, and copy machines.<\/p>\n<p>Sample processing services include standard plasma, serum, and buffy coat separation, PBMC<br \/>\nisolation by Ficoll separation, granulocyte isolation, solid tissue formalin fixing, snap-freezing of<br \/>\ntissue and cells, and cryopreservation capabilities. The laboratory equipment is maintained in<br \/>\naccordance with the standards set by Good Laboratory Practice (GLP) and CAP.<\/p>\n<p>Please contact <a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\" target=\"_blank\" rel=\"noopener\">Manoj Menon<\/a> for more information.\n<\/div>\n<\/div>\n<div class=\"su-spoiler su-spoiler-style-default su-spoiler-icon-caret su-spoiler-closed\" data-scroll-offset=\"0\" data-anchor-in-url=\"no\">\n<div class=\"su-spoiler-title\" role=\"button\"><span class=\"su-spoiler-icon\"><\/span>HIVAM Research Consultation<\/div>\n<div class=\"su-spoiler-content su-u-clearfix su-u-trim\">\nThe HIVAM Core provides consultation services for researchers performing clinical or population science HIVAM research. Please contact us if you are planning assay development. To request a consultation, please email\u00a0<a href=\"mailto:tuldrick@fredhutch.org\">tuldrick@fredhutch.org<\/a>.<\/p>\n<p>Please contact\u00a0<a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\" target=\"_blank\" rel=\"noopener\">Manoj Menon<\/a>\u00a0for more information.\n<\/div>\n<\/div>\n<div class=\"su-spoiler su-spoiler-style-default su-spoiler-icon-caret su-spoiler-closed\" data-scroll-offset=\"0\" data-anchor-in-url=\"no\">\n<div class=\"su-spoiler-title\" role=\"button\"><span class=\"su-spoiler-icon\"><\/span>Human Papillomavirus Genotyping (HCRI-Uganda)<\/div>\n<div class=\"su-spoiler-content su-u-clearfix su-u-trim\">\nThrough 2020, we have employed the Roche Linear Array HPV Genotyping Test for HPV-<br \/>\nassociated malignancy research. This commercial assay is based on four major processes:<br \/>\nspecimen preparation\/DNA Extraction using the Qiagen MinElute Extraction Kit and Vacuum<br \/>\nSystem; PCR Amplification of the HPV polymorphic L1 region using pool of HPV Primers;<br \/>\nhybridization of the amplified products to oligonucleotide probes; and detection of the probe-<br \/>\nbound amplified products by colorimetric determination. This assay has the ability to detect<br \/>\nHPV DNA of 37 anogenital HPV types.<\/p>\n<p>These HPV genotypes included: 6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 45, 51, 52, 53, 54, 55,<br \/>\n56, 58, 59, 61, 62, 64, 66, 67, 68, 69, 70, 71, 72, 73 (MM9), 81, 82 (MM4), 83 (MM7), 84 (MM8),<br \/>\nIS39, and CP6108.<\/p>\n<p>The ideal sample type is a cervical, genital, or rectal brush or swab collected and stored in a<br \/>\nPCR Buffer such as the Roche PCR Cell Collection Media. As of 2020, this assay is being discontinued by Roche diagnostics no longer available. The HIVAM Core is pursuing a comparable assay to replace this legacy assay at our site for 2021.<\/p>\n<p>Please contact\u00a0<a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\" target=\"_blank\" rel=\"noopener\">Manoj Menon<\/a>\u00a0for more information.\n<\/div>\n<\/div>\n<div class=\"su-spoiler su-spoiler-style-default su-spoiler-icon-caret su-spoiler-closed\" data-scroll-offset=\"0\" data-anchor-in-url=\"no\">\n<div class=\"su-spoiler-title\" role=\"button\"><span class=\"su-spoiler-icon\"><\/span>Kaposi Sarcoma Herpesvirus (KSHV) LANA Immunohistochemistry (HCRI-Uganda)<\/div>\n<div class=\"su-spoiler-content su-u-clearfix su-u-trim\">\nImmunohistochemistry (IHC) for KSHV latency associated nuclear protein (LANA) helps<br \/>\nvisualize the localization and distribution of KSHV infected cells in tissue sections based on the<br \/>\nantigen-antibody binding reaction. The laboratory follows manual processes of IHC staining of<br \/>\nLANA utilizing the Novocastra liquid mouse monoclonal antibody from Leica, NCL-L-<br \/>\nHHV-8-LNA (Clone13B10, class IgG1).<\/p>\n<p>Please contact\u00a0<a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\" target=\"_blank\" rel=\"noopener\">Manoj Menon<\/a>\u00a0for more information.\n<\/div>\n<\/div>\n<div class=\"su-spoiler su-spoiler-style-default su-spoiler-icon-caret su-spoiler-closed\" data-scroll-offset=\"0\" data-anchor-in-url=\"no\">\n<div class=\"su-spoiler-title\" role=\"button\"><span class=\"su-spoiler-icon\"><\/span>Real-Time Quantitative Epstein Barr Virus (EBV) PCR (HCRI-Uganda)<\/div>\n<div class=\"su-spoiler-content su-u-clearfix su-u-trim\">\nEBV is a necessary etiology agent of endemic Burkitt\u2019s lymphoma, as well as a range of<br \/>\naggressive B-cell lymphomas that are strongly associated with HIV, including plasmablastic<br \/>\nlymphoma, AIDS-associated primary CNS lymphoma and a proportion of cases of classical<br \/>\nHodgkin lymphoma, diffuse large B-cell lymphoma and primary effusion lymphoma.<\/p>\n<p>EBV RT-PCR assay can be performed on clinical samples including saliva, genital secretion,<br \/>\nCSF, plasma, serum, body fluids and tissues. Viral DNA is extracted and quantified using PCR<br \/>\ntechniques. DNA extraction is performed using Qiagen chemistry and single column procedure.<br \/>\nPCR is performed on a high-throughput ABI 7900 thermocycler, in addition to two new 7500<br \/>\nsystems. To date, more than 75,000 PCR tests have been resulted in this laboratory, which<br \/>\nundergoes regular Quality Control audits by the Seattle-based molecular diagnostics lab.<br \/>\nThe Real-Time Taqman PCR assay utilizes fluorescent labeled probes to amplify, detect and<br \/>\nquantify EBV. Primers and probes specific to the BALF5 region of the EBV genome. The beta-<br \/>\nGlobin region of the human genome may be used to quantify cellular content of the specimen.<br \/>\nThese assays were designed and tested for sensitivity and specificity at the University of<br \/>\nWashington Molecular Diagnostic Lab in Seattle, Washington, USA. An internal control is<br \/>\nspiked into each PCR reaction to ensure that no non-specific inhibition of the reaction has taken<br \/>\nplace. A negative result is accepted only if the internal control amplification is detected.<br \/>\nInhibited samples are re-extracted or chelexed and the analysis repeated.<\/p>\n<p>Please contact\u00a0<a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\" target=\"_blank\" rel=\"noopener\">Manoj Menon<\/a>\u00a0for more information.\n<\/div>\n<\/div>\n<div class=\"su-spoiler su-spoiler-style-default su-spoiler-icon-caret su-spoiler-closed\" data-scroll-offset=\"0\" data-anchor-in-url=\"no\">\n<div class=\"su-spoiler-title\" role=\"button\"><span class=\"su-spoiler-icon\"><\/span>Real-Time Quantitative Kaposi Sarcoma Herpesvirus (KSHV) PCR (HCRI-Uganda)<\/div>\n<div class=\"su-spoiler-content su-u-clearfix su-u-trim\">\nKSHV is the necessary but insufficient infectious etiologic agent of Kaposi sarcoma (KS), a form<br \/>\nof multicentric Castleman disease (KSHV-MCD) and primary effusion lymphoma (PEL). KSHV<br \/>\nprevalence is greater than 60% in the general population in Uganda. KSHV PCR is available for<br \/>\nresearch on these important HIVAM.<\/p>\n<p>KSHV RT-PCR assay can be performed on clinical samples including saliva, genital secretion,<br \/>\nCSF, plasma, serum, body fluids and tissues. Viral DNA is extracted and quantified using PCR<br \/>\ntechniques. DNA extraction is performed using Qiagen chemistry and single column procedure.<br \/>\nPCR is performed on a high-throughput ABI 7900 thermocycler, in addition to two new 7500<br \/>\nsystems. To date, more than 75,000 PCR tests have been resulted in this laboratory, which<br \/>\nundergoes regular Quality Control audits by the Seattle-based molecular diagnostics lab.<\/p>\n<p>The Real-Time Taqman PCR assay utilizes fluorescent labeled probes to amplify, detect and<br \/>\nquantify KSHV. Primers and probes specific to the ORF73 and T.07-K12 regions of the KSHV<br \/>\ngenome. The beta-Globin region of the human genome may be used to quantify cellular content<br \/>\nof the specimen. These assays were designed and tested for sensitivity and specificity at the<br \/>\nUniversity of Washington Molecular Diagnostic Lab in Seattle, Washington, USA. An internal<br \/>\ncontrol is spiked into each PCR reaction to ensure that no non-specific inhibition of the reaction<br \/>\nhas taken place. A negative result is accepted only if the internal control amplification is<br \/>\ndetected. Inhibited samples are re-extracted or chelexed and the analysis repeated.<\/p>\n<p>Please contact\u00a0<a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\" target=\"_blank\" rel=\"noopener\">Manoj Menon<\/a>\u00a0for more information.\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"tab-pane fade show\" id=\"tab-tour-2\" role=\"tabpanel\" aria-labelledby=\"title-tab-tour-2\" tabindex=\"0\">\nThe BPIN Core continues to cultivate research in the Seattle biomedical community through the provision of assistance with lab assay development, consultation, and data tools. Additionally, the number of researchers within this field is growing with many of our junior investigators and next generation leaders initiating independent research careers in the field of HIVAM with the support of UW\/Fred Hutch CFAR. Further, the NIH funding base for research in HIVAM has grown to over $15 million, and several grants, including K23s, R21s, R01s, P01s, and U54s have been awarded to HIVAM members, furthering CFAR\u2019s mission of adding value to the local research community.\n<\/div>\n<div class=\"tab-pane fade show\" id=\"tab-tour-3\" role=\"tabpanel\" aria-labelledby=\"title-tab-tour-3\" tabindex=\"0\">\n<p><em>Director<\/em><br \/>\n<a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\">Manoj Menon<\/a>, MD, MPH<br \/>\n<a href=\"mailto:mmenon@fredhutch.org\">mmenon@fredhutch.org<\/a><\/p>\n<p><em>Associate Director<\/em><br \/>\n<a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/phipps-warren.html\">Warren Phipps<\/a>, MD, MPH<br \/>\n<a href=\"mailto:wtphipps@fredhutch.org\">wtphipps@fredhutch.org<\/a><\/p>\n<p><em>Core Manager<\/em><br \/>\nTBD\n<\/div>\n<div class=\"tab-pane fade show\" id=\"tab-tour-4\" role=\"tabpanel\" aria-labelledby=\"title-tab-tour-4\" tabindex=\"0\">\n<p><a href=\"https:\/\/www.fredhutch.org\/en\/faculty-lab-directory\/menon-manoj.html\">Manoj Menon<\/a>, MD, MPH<br \/>\n<a href=\"mailto:mmenon@fredhutch.org\">mmenon@fredhutch.org<\/a><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Cancer has become the leading cause of death among persons with HIV infection worldwide. Kaposi sarcoma, non-Hodgkin lymphoma, and cervical cancer were recognized as AIDS-Defining Malignancies (ADM) early in the epidemic. In the setting of broadly available ART, cancer now impacts persons living with HIV both at the time of diagnosis and as a consequence of long-term HIV infection. In addition to ADM, people living with HIV are at increased risk of a range of cancers, including lung cancer, anal&#8230;<\/p>\n","protected":false},"author":2,"featured_media":824,"parent":109,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"templates\/template-small-hero.php","meta":{"footnotes":""},"class_list":["post-823","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/pages\/823","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/comments?post=823"}],"version-history":[{"count":12,"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/pages\/823\/revisions"}],"predecessor-version":[{"id":2361,"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/pages\/823\/revisions\/2361"}],"up":[{"embeddable":true,"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/pages\/109"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/media\/824"}],"wp:attachment":[{"href":"https:\/\/depts.washington.edu\/cfar\/wp-json\/wp\/v2\/media?parent=823"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}