HIV/AIDS Genomics: Advances in Therapy & Tests
RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection
Hu W, et al. PNAS, Jul 21, 2014.
Hu W, et al. PNAS, Jul 21, 2014.
Genome editing cuts out HIV
Grens K. The Scientist, Jul 21, 2014.
Grens K. The Scientist, Jul 21, 2014.
Gene researchers work to engineer HIV-resistant cells
Hampton T. JAMA, Jul 9, 2014.
Hampton T. JAMA, Jul 9, 2014.
Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV
Tebas P, et al. N Engl J Med. 2014 Mar 6;370(10):901-10.
Tebas P, et al. N Engl J Med. 2014 Mar 6;370(10):901-10.
Promising results from HIV gene editing therapy, PHG Foundation, Mar 10
PHG Foundation, Mar 10Check out guidelines on genomic tests associated with HIV/AIDS treatment, from the CDC evidence-based table
HLA-B*5701/abacavir | |
CCR5-tropic HIV-1 /maraviroc |
Diagnostic accuracy of HLA-B*57:01 screening for the prediction of abacavir hypersensitivity and clinical utility of the test: a meta-analytic review
Cargnin S, et al. Pharmacogenomics. 2014;15(7):963-76.
Cargnin S, et al. Pharmacogenomics. 2014;15(7):963-76.
Did you know? 1799 genes have been reported in relation to HIV risk & outcomes including 33 genomewide association studies. To find out more, visit the HuGE Navigator
Genetic Testing
Genomic Tests and Family History by Levels of Evidence
The CDC Office of Public Health Genomics ranks the following list for levels of evidence of genomic tests and family health history in practice . This approach was based on a paper byKhoury and updated in accordance with criteria presented by a 2014 paper in Clinical Pharmacology and Therapeutics. The criteria are shown in the following figure to provide additional information to our readers.This list is updated on an ongoing basis andprovided only for informational purposes to researchers, healthcare providers, public health programs and others.
and updated in accordance with criteria presented by a 2014 paper in Clinical Pharmacology and Therapeutics. The criteria are shown in the following figure to provide additional information to our readers.This list is updated on an ongoing basis andprovided only for informational purposes to researchers, healthcare providers, public health programs and others.Green
- FDA label requires use of test to inform choice or dose of a drug
- CMS covers testing
- Clinical practice guidelines based on systematic review supports testing
Yellow
- FDA label mentions biomarkers*
- CMS coverage with evidence development
- Clinical practice guideline, not based on systematic review, supports use of test
- Clinical practice guideline finds insufficient evidence but does not discourage use of test
- Systematic review, without clinical practice guideline, supports use of test
- Systematic review finds insufficient evidence but does not discourage use of test
- Clinical practice guideline recommends dosage adjustment, but does not address testing
Red
- FDA label cautions against use
- CMS decision against coverage
- Clinical practice guideline recommends against use of test
- Clinical practice guideline finds insufficient evidence and discourages use of test
- Systematic review recommends against use
- Systematic review finds insufficient evidence and discourages use
- Evidence available only from published studies without systematic reviews, clinical practice guidelines, FDA label or CMS labels coverage decision
*Can be reassigned to Green of Red of one or more conditions in these categories apply
Tier 1/Green category: represents genomic and family health history applications which have a base of synthesized evidence supporting implementation into practice.
| Gene, Gene/Drug, Test, or Family History | Disorder/Indication | Use* | Synthesized Evidence Sources |
|---|---|---|---|
| Cancer—Breast/Ovarian | |||
| family history of breast/ovarian or other types of BRCA-related cancer | hereditary breast and ovarian cancer in women | risk prediction for referral for BRCA genetic counseling | USPSTF (2013)NCCN Task Force (2011) |
| first-degree family history of breast cancer | hereditary breast and ovarian cancer in women | risk prediction, chemoprevention | USPSTF (2013) |
| family history of known breast/ovarian cancer with deleterious BRCA mutation | hereditary breast and ovarian cancer in women | risk prediction; referral to counseling for BRCA genetic testing | USPSTF (2013) |
| HER2/trastuzumab | invasive breast cancer | PGx | NICE  [PDF 2.00 MB](2009)ASCO (2007)FDA-Device (2013)FDA-PGx Drug Information (2013) |
| HER2/pertuzumab | invasive breast cancer | PGx | FDA-Device (2013)FDA-PGx Drug Information (2013) |
| HER2/ado-trastuzumab emtansine | metastatic breast cancer | PGx | FDA-PGx Drug Information(2013) |
| HER2/everolimus | advanced HR+ HER2- breast cancer | PGx | FDA-PGx Drug Information(2013) |
| HER2/lapatinib (in combination with capecitabine or letrozole) | advanced or metastatic breast cancer | PGx | FDA-PGx Drug Information(2013) |
| HER2 | invasive breast cancer | PGx | ASCO/CAP (2007)NICE [PDF 178.88 KB](2009) |
| ER /fulvestrant | metastatic breast cancer | PGx | FDA-PGx Drug Information(2012) |
| ER/exemestane | ER+ early breast cancer | PGx | FDA-PGx Drug Information (2013)NICE [PDF 178.88 KB](2009) |
| ER/anastrozole or letrozole | ER+ early invasive breast cancer | PGx | NICE [PDF 178.88 KB](2009) |
| ER and PgR | invasive breast cancer, breast cancer recurrences | PGx | ASCO/CAP (2010)NCCN Task Force (2011) |
| Oncotype DX® adjuvant chemotherapy | ER+/LN-/HER2- breast cancer, intermediate risk of recurrence | prognostic; guiding decision-making: adjuvant chemotherapy | NICE (2013)NCCN Task Force (2011) |
| Cancer—Colorectal | |||
| Testing for Lynch syndrome | newly diagnosed colorectal cancer | screening, cascade testing of relatives | EGAPP (2009) |
| Testing for Lynch syndrome | known Lynch syndrome in family | diagnostic, screening | EGAPP (2009) NCCN : Genetic/Familial High-Risk Assessment - Colorectal (2014) |
| KRAS/cetuximab, panitumumab | metastatic colorectal cancer | PGx | EGAPP [PDF 456.16 KB](2013)NCCN (2011)ASCO (2009)FDA-PGx Drug Information (2013) |
| Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5 or CEA) | invasive colorectal cancer | prognostic | ASCO/CAP (2006)NCCN [PDF 1.27 MB](2013)NCCN Task Force (2011) |
| Cancer—Gastric | |||
| HER2/trastuzumab | gastric or gastroesophageal junction adenocarcinoma | PGx | FDA-Device (2013)FDA-PGx Drug Information (2013) |
| c-Kit protein (CD 117)/imatinib | gastrointestinal stromal tumors | PGx | FDA-Device (2013)FDA-PGx Drug Information (2013) |
| Cancer—Leukemia/lymphoma | |||
| Philadelphia chromosome, T315I mutation/dasatinib | chronic myeloid leukemia, acute lymphoblastic leukemia | PGx; diagnostic | FDA-PGx Drug Information(2013) |
| Philadelphia chromosome/imatinib | chronic myeloid leukemia, acute lymphoblastic leukemia | PGx; diagnostic | FDA-PGx Drug Information(2013) |
| Philadelphia chromosome/bosutinib | chronic myelogenous leukemia | PGx; diagnostic | FDA-PGx Drug Information (2013) |
| Philadelphia chromosome/nilotinib | chronic myeloid leukemia | PGx; diagnostic | FDA-PGx Drug Information(2013) |
| PML/RARα/tretinoin | acute promyelocytic leukemia | PGx | FDA-PGx Drug Information(2004) |
| PML/RARα/arsenic trioxide | acute promyelocytic leukemia | PGx | FDA-PGx Drug Information(2010) |
| PDGFRB/imatinib | myelodysplastic/ myeloproliferative diseases | PGx | FDA-PGx Drug Information (2013) |
| CD25/denileukin diftitox | persistent or recurrent cutaneous T-cell lymphoma | PGx | FDA-PGx Drug Information (2011) |
| CD20/tositumomab | Non-Hodgkin's lymphoma | PGx | FDA-PGx Drug Information (2012) |
| G6PD/rasburicase | leukemia, lymphoma, solid tumor malignancies | PGx, pretreatment screening in patients at higher risk for G6PD deficiency (e.g., African or Mediterranean ancestry) | FDA-PGx Drug Information CPIC(2009) (2014) |
| Chromosome 5q deletion/lenalidomide | transfusion-dependent anemia due to low-or intermediate-1-risk myelodysplastic syndromes associated with a deletion 5q | PGx | FDA-PGx Drug Information (2013) |
| Cancer—Lung | |||
| EGFR (exon 19 deletions and exon 21 (L858R) substitution mutations)/afatinib | metastatic non-small-cell lung cancer | PGx | FDA-Device (2013)FDA-PGx Drug Information (2013) |
| EGFR (exon 19 deletions and exon 21 (L858R) substitution mutations)/erlotinib | locally advanced or metastatic non-small-cell lung cancer | PGx | NICE [PDF 189.11 KB](2012)NCCN Task Force (2011)FDA-Device (2013)FDA-PGx Drug Information (2013) |
| ALK gene rearrangement/crizotinib | non-small cell lung cancer | PGx | FDA-Device (2013)FDA-PGx Drug Information (2013)NCCN Task Force (2011)NCCN Guideline [PDF 1.61 MB] (2013) |
| Cancer—Melanoma | |||
| BRAF V600E/K /trametinib | unresectable or metastatic melanoma | PGx | FDA-PGx Drug Information (2013)FDA-Device (2013) |
| BRAF V600E/dabrafenib | unresectable or metastatic melanoma | PGx | FDA-PGx Drug Information (2013)FDA-Device (2013) |
| BRAFV600E/vemurafenib | unresectable or metastatic melanoma | PGx | NICE (2012)FDA-PGx Drug Information (2013)FDA-Device (2013) |
| Cardiovascular disease | |||
| DNA testing and LDL-C concentration measurement | familial hypercholesterolemia | cascade testing of relatives of people diagnosed with FH | NICE [PDF 201.05 KB](2008) |
| family history of cardiovascular disease before age 50 years in male relatives and age 60 years in female relatives | cholesterol screening | risk prediction | USPSTF (2008) |
| Infectious disease | |||
| HLA-B*5701/abacavir | HIV | PGx | CPIC (2014)FDA-PGx Drug Information (2013) |
| CCR5-tropic HIV-1 /maraviroc | HIV | PGx | FDA-PGx Drug Information (2013)HHS Panel [PDF 1.46 MB](2013) |
| Other | |||
| CFTR (G551D)/ivacaftor | cystic fibrosis | PGx | FDA-PGx Drug Information(2012) |
| HLA-B*1502/carbamazepine | epilepsy, trigeminal neuralgia; pretreatment screening for those with ancestry in populations genetically at-risk for certain serious dermatologic reactions | PGx, pretreatment screening for those with ancestry in populations genetically at-risk for certain serious dermatologic reactions | FDA-PGx Drug Information(2013) |
| CYP2D6/pimozide | Tourette’s disorder | PGx-dose | FDA-PGx Drug Information(2011) |
| CYP2D6/tetrabenazine | chorea associated with Huntington’s disease | PGx-dose | FDA-PGx Drug Information(2011) |
| G6PD/pegloticase | chronic gout in adults refractory to conventional therapy | PGx, pretreatment screening in patients at higher risk for G6PD deficiency (e.g., African or Mediterranean ancestry) | FDA-PGx Drug Information(2012) |
| Parental history of hip fracture | osteoporosis screening in women | risk prediction | USPSTF (2011) |
| family history, especially siblings, with hereditary hemochromatosis | hereditary hemochromatosis | risk prediction; counseling for genetic testing among asymptomatic people | USPSTF (2006) |
| newborn screening panel | 31 core conditions | screening | SACHDNC (2013) |
*Pharmacogenomic applications have been classified in the Use column as either PGx (which may relate to drug choice, prevention of adverse events, or other uses of the information gained through testing), or PGx-dose (when specific dosing-related guidance is provided, or mention of a potential effect on dose is noted in the evidence sources cited). Additional Use categories include: screening, cascade testing, risk prediction, diagnostic, and prognostic.
Source Abbreviations: Agency for Healthcare Research and Quality (AHRQ), American College of Medical Genetics and Genomics (ACMG), American Society of Clinical Oncology (ASCO), Centers for Medicare and Medicaid Services (CMS), Clinical Pharmacogenetics Implementation Consortium (CPIC), Evaluation of Genomic Applications in Practice and Prevention (EGAPP), National Comprehensive Cancer Network (NCCN), National Institute for Health and Care Excellence (NICE), National Institutes of Health (NIH), Secretary’s Advisory Committee on Heritable Disorders in Newborns and Children (SACHDNC), US Department of Health and Human Services (DHHS), US Food and Drug Administration (FDA), United States Preventive Services Task Force (USPSTF)
Other Abbreviations: estrogen receptor (ER), progesterone receptor (PgR), pharmacogenomics (PGx), single-nucleotide polymorphism (SNP)
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