Study Shows Potential of Whole Exome Sequencing for Targeting Therapy Based on Tumor Genomics

Researchers at Weill Cornell Medical College-New York Presbyterian Hospital in New York City recently demonstrated the potential of whole exome sequencing (WES) to identify cancer mutations and guide treatment decisions (JAMA Oncology 2015;1:466-74). “This precision medicine trial provides a rigorous proof of principle for developing a precision medicine approach to clinical cancer care with the capability to identify novel biomarkers of response and therapeutic targets,” wrote the authors.

The study involved 97 cancer patients with advanced, treatment-resistant cancer. The investigators tested DNA in patients’ tumor and normal tissue using a WES test they had developed and validated, called EXaCT-1. The authors found that more than 90% of patients had actionable or biologically informative mutations. Overall, they discovered an average of 16 mutations per patient from 154 tumors.

The EXaCT-1 test had 100% sensitivity and specificity in detecting clinically relevant HER2 copy number changes, BRAF, KRAS, EGFR, JAK2 point mutations and EGFR indels, with no significant differences between formalin-fixed paraffin-embedded and fresh-frozen specimens independent of DNA quantity. The researchers needed at least 200 ng of DNA for WES.

The authors used an analytical algorithm to interrogate and prioritize 94 alterations in 49 actionable and clinically relevant genes, designated as category 1 because they already are known to respond to available drugs. They designated another 508 alterations as category 2, meaning therapies targeting them are in clinical or preclinical development, or that they are considered driver mutations and therefore potentially actionable. The investigators classified as category 3 all other genetic alterations of unknown significance. Overall, 16 category 1, 98 category 2 and 1,474 category 3 mutations were evident across tumor types.

Even with all the information available from WES, patients had access to therapies through other clinical trials or off-label use of drugs, so just five received treatment guided by WES. WES also explained one patient’s exceptional response to therapy during the course of the trial.

“Most institutions are using focused or panel sequencing to look at a few hot spot mutation areas in cancer,” said senior author Mark Rubin. “But we believe that [WES], which tests more than 21,000 genes ... is ideal for patients with advanced cancer where we don’t know where the mutations of resistance are.”

Low Urine Albumin/Creatinine Ratio Reliably Detects Antiviral Nephrotoxicity in HIV-infected Patients

Low urine albumin/creatinine ratio (uACR) reliably indicates tenofovir disoproxil fumarate (TDF) nephrotoxicity in HIV-infected patients and could be a means of discerning proximal tubular injury from glomerular injury (AIDS 2015;29:941-46). However, dipstick urinalysis may be unreliable in TDF nephrotoxicity due to the predominance of nonalbumin proteinuria.

TDF is an antiviral therapy used in HIV infection and hepatitis B infection, but it can cause nephrotoxicity, particularly renal tubular injury. The authors hypothesized that pre­dominance of nonalbumin proteinuria—indicating tubular injury—could distinguish TDF nephrotoxicity from other types of renal damage associated with HIV infection.

The authors reviewed medical records and biopsy reports for 43 biopsy-proven TDF nephrotoxicity cases versus control cases of patients with HIV who had not taken TDF but had undergone renal biopsy. The latter had significantly higher urine albumin-to-protein ratio versus patients with TDF nephrotoxicity (0.65 versus 0.17), confirming that TDF nephrotoxicity is primarily associated with nonalbumin proteinuria, according to the authors. However, 40% of patients with TDF nephrotoxicity had 1+ proteinuria or less via dipstick urinalysis, while several cases had 0 to trace amounts. Given these findings, the authors recommended measuring total urine protein with urine protein/creatinine ratio, followed by urine albumin-to-protein ratio to distinguish tubular from glomerular injury.

Little Race-Based Difference in Free Vitamin D Levels; Considerable Variability in Vitamin D Binding Protein Assays

Researchers reported nearly identical values of free vitamin D (25(OH)D) in age- and body mass index-matched postmenopausal African-American and Caucasian women (5.25 ±1.2 ng/mL versus 5.25 ±1.3 ng/mL, respectively) (J Clin Endocrinolo Metab 2015; At the same time, they found lower total 25(OH)D in African-American women versus in Caucasian women, with mean values 19.5 ng/mL versus 26.9 ng/mL, respectively. In addition, they observed discordant vitamin D binding protein (VDBP) results measured with a monoclonal-based enzyme-linked immunosorbent assay (ELISA) versus a polyclonal-based ELISA.

The findings add to emerging research on the paradox of African-Americans having low serum 25(OH)D levels—considered a risk for poor bone health—but superior bone health in comparison to Caucasians. Recent research found that while African-Americans had lower serum total 25(OH)D than Caucasians, their bioavailable 25(OH)D was about the same. However, that study used an indirect method to estimate free 25(OH)D.

With new methods available to directly assess free 25(OH)D, the authors sought to compare free 25(OH)D levels in African-Americans versus Caucasians. The investigators measured the participants’ total 25(OH)D, albumin, 1,25-dihydroxyvitamin­ D, calcium, parathyroid hormone, C-terminal telopeptides of type I collagen, VDBP, and free 25(OH)D.

They concluded that it would be preferable to directly measure 25(OH)D, given the divergent VDBP results across assays, and variability in VDBP associated with obesity, liver disease, and other conditions.

APOE ε4-positivity Linked to Abnormal CSF Biomarkers Levels in Individuals With Significant Memory Concerns

Alzheimer’s Disease Neuroimaging Initiative (ADNI) researchers reported that older individuals with significant memory concerns (SMC) who carry the APOE ε4 gene allele show abnormal changes in cerebrospinal fluid (CSF) biomarkers in comparison to APOE ε4 non-carriers (Alzheimers Dement 2015; How­ever, APOE ε4 carriers did not exhibit glucose hypometabolism in the brain or medial temporal lobe atrophy.

The findings add to evidence that APOE is a “major mediator” of CSF amyloid beta (Aβ)1-42 and tau abnormalities in individuals with SMC, according to the authors. The study also parallels other research which indicates that (Aβ)1-42 and tau abnormalities develop in advance of cognitive symptoms. That the SMC subjects did not exhibit glucose hypometabolism or brain atrophy suggests that these conditions might be linked to cognitive decline.

The study involved cognitively normal, SMC, and early mild cognitive impairment ADNI participants who were divided based on APOE ε4 carrier status, with those with one or more ε4 alleles considered APOE ε4-positive. 

In comparison to APOE ε4-negative subjects, CSF (Aβ)1-42 levels in SMC APOE ε4-positive participants were significantly lower, while CSF phosphorylated tau levels were significantly higher. Researchers observed the greatest CSF (Aβ)1-42 and tau abnormalities in SMC APOE ε4-positive participants who also were positive for cerebral amyloid via FDG positron emission tomography.