Rajyasree Emmadi

Molecular Methods and Platforms for Infectious Diseases Testing: A Review of FDA-Approved and Cleared Assays

The superior sensitivity and specificity associated with the use of molecular assays has greatly improved the field of infectious disease diagnostics by providing clinicians with results that are both accurate and rapidly obtained. Herein, we review molecularly based infectious disease diagnostic tests that are Food and Drug Administration approved or cleared and commercially available in the United States as of December 31, 2010. We describe specific assays and their performance, as stated in the Food and Drug Administrations Summary of Safety and Effectiveness Data or the Office of In Vitro Diagnostic Device Evaluation and Safetys decision summaries, product inserts, or peer-reviewed literature. We summarize indications for testing, limitations, and challenges related to implementation in a clinical laboratory setting for a wide variety of common pathogens. The information presented in this review will be particularly useful for laboratories that plan to implement or expand their molecular offerings in the near term.

Excess of Proximal Microsatellite-Stable Colorectal Cancer in African Americans from a Multiethnic Study

Purpose: African Americans (AA) have the highest incidence of colorectal cancer compared with other U.S. populations and more proximal colorectal cancers. The objective is to elucidate the basis of these cancer disparities. Experimental design: Of note, 566 AA and 328 non-Hispanic White (NHW) colorectal cancers were ascertained in five Chicago hospitals. Clinical and exposure data were collected. Microsatellite instability (MSI) and BRAF (V600E) and KRAS mutations were tested. Statistical significance of categorical variables was tested by the Fisher exact test or logistic regression and age by the Mann–Whitney U test. Results: Over a 10-year period, the median age at diagnosis significantly decreased for both AAs (68–61; P < 0.01) and NHWs (64.5– 62; P = 0.04); more AA patients were diagnosed before age 50 than NHWs (22% vs. 15%; P = 0.01). AAs had more proximal colorectal cancer than NHWs (49.5% vs. 33.7%; P < 0.01), but overall frequencies of MSI, BRAF and KRAS mutations were not different nor were they different by location in the colon. Proximal colorectal cancers often presented with lymphocytic infiltrate (P < 0.01) and were diagnosed at older ages (P = 0.02). Smoking, drinking, and obesity were less common in this group, but results were not statistically significant. Conclusions: Patients with colorectal cancer have gotten progressively younger. The excess of colorectal cancer in AAs predominantly consists of more proximal, microsatellite stable tumors, commonly presenting lymphocytic infiltrate and less often associated with toxic exposures or a higher BMI. Younger AAs had more distal colorectal cancers than older ones. These data suggest two different mechanisms driving younger age and proximal location of colorectal cancers in AAs. Clin Cancer Res; 20(18); 4962–70. ©2014 AACR.

High definition infrared spectroscopic imaging for lymph node histopathology.

Chemical imaging is a rapidly emerging field in which molecular information within samples can be used to predict biological function and recognize disease without the use of stains or manual identification. In Fourier transform infrared (FT-IR) spectroscopic imaging, molecular absorption contrast provides a large signal relative to noise. Due to the long mid-IR wavelengths and sub-optimal instrument design, however, pixel sizes have historically been much larger than cells. This limits both the accuracy of the technique in identifying small regions, as well as the ability to visualize single cells. Here we obtain data with micron-sized sampling using a tabletop FT-IR instrument, and demonstrate that the high-definition (HD) data lead to accurate identification of multiple cells in lymph nodes that was not previously possible. Highly accurate recognition of eight distinct classes - naïve and memory B cells, T cells, erythrocytes, connective tissue, fibrovascular network, smooth muscle, and light and dark zone activated B cells was achieved in healthy, reactive, and malignant lymph node biopsies using a random forest classifier. The results demonstrate that cells currently identifiable only through immunohistochemical stains and cumbersome manual recognition of optical microscopy images can now be distinguished to a similar level through a single IR spectroscopic image from a lymph node biopsy.

The Spectrum of Clinical Utilities in Molecular Pathology Testing Procedures for Inherited Conditions and Cancer: A Report of the Association for Molecular Pathology

Clinical utility describes the benefits of each laboratory test for that patient. Many stakeholders have adopted narrow definitions for the clinical utility of molecular testing as applied to targeted pharmacotherapy in oncology, regardless of the population tested or the purpose of the testing. This definition does not address all of the important applications of molecular diagnostic testing. Definitions consistent with a patient-centered approach emphasize and recognize that a clinical test results utility depends on the context in which it is used and are particularly relevant to molecular diagnostic testing because of the nature of the information they provide. Debates surrounding levels and types of evidence needed to properly evaluate the clinical value of molecular diagnostics are increasingly important because the growing body of knowledge, stemming from the increase of genomic medicine, provides many new opportunities for molecular testing to improve health care. We address the challenges in defining the clinical utility of molecular diagnostics for inherited diseases or cancer and provide assessment recommendations. Starting with a modified analytic validity, clinical validity, clinical utility, and ethical, legal, and social implications model for addressing clinical utility of molecular diagnostics with a variety of testing purposes, we recommend promotion of patient-centered definitions of clinical utility that appropriately recognize the valuable contribution of molecular diagnostic testing to improve patient care.

Evaluation of Resection Margins in Breast Conservation Therapy: The Pathology Perspective—Past, Present, and Future

Tumor surgical resection margin status is important for any malignant lesion. When this occurs in conjunction with efforts to preserve or conserve the afflicted organ, these margins become extremely important. With the demonstration of no difference in overall survival between mastectomy versus lumpectomy and radiation for breast carcinoma, there is a definite trend toward smaller resections combined with radiation, constituting “breast-conserving therapy.” Tumor-free margins are therefore key to the success of this treatment protocol. We discuss the various aspects of margin status in this setting, from a pathology perspective, incorporating the past and current practices with a brief glimpse of emerging future techniques.

No clinical benefit from routine histologic examination of stapler doughnuts at low anterior resection for rectal cancer

Background. The aim of this study was to evaluate the clinical utility and cost‐effectiveness of routine histologic examination of the doughnuts from stapled anastomoses in patients undergoing a low anterior resection for rectal cancer. Methods. We performed a retrospective review of 486 patients who underwent a low anterior resection with stapled anastomosis for rectal cancer between 2002 and 2015 at 3 institutions. Pathologic findings in the doughnuts and their impact on patient management were recorded. Tumor characteristics that may influence how often doughnuts were included in the pathology report were analyzed. An approximate cost of histologic examination of doughnuts was also calculated. Results. A total of 412 patients (85%) had doughnuts included in their pathology reports. Two patients had cancer cells in their doughnuts, and both patients had a positive distal margin in their primary tumor specimen; 33 patients had benign findings in their doughnuts. Pathologic examination of the doughnut did not change clinical management in any patient. Patients with rectosigmoid tumors were less likely to have their doughnuts included in the pathology report compared to patients with low tumors (P = .003). Doughnuts were not bundled with the primary tumor specimen in 374 (77%) of our patients; in these patients, pathologic analysis of the doughnut added an additional cost of approximately

Correlative Analysis of miRNA Expression and Oncotype Dx Recurrence Score in Estrogen Receptor Positive Breast Carcinomas

643 per specimen. Conclusion. This study demonstrates no clinical benefit in sending anastomotic doughnuts for histopathologic evaluation after performing a low anterior resection with a stapled anastomosis for rectal cancer. Overall cost may be decreased if doughnuts are not analyzed or if they are bundled with the primary tumor specimen.

Third‐harmonic generation imaging of breast tissue biopsies

Altered expression of miRNAs has been observed in many types of cancer, including breast cancer, and shown to contribute to cancer growth, aggressiveness, and response to therapies. In this pilot study, we investigated the possible correlation of miRNAs with risk of recurrence of estrogen receptor positive, lymph node-negative mammary carcinomas as determined by the Oncotype DX® Breast Cancer assay. To accomplish this, we extracted RNA from a collection of breast carcinomas that had previously been analyzed by Oncotype DX®. Multiple Let-7 family members were negatively correlated with the recurrence score (RS), which is consistent with their tumor suppressor properties. Additional miRNAs were found to positively correlate with RS, including miR-377-5p, miR-633b, miR-548t and miR-3648. Pathway analysis of putative and validated targets suggests that these miRNAs may have a diverse range of functions that may contribute to tumor recurrence. Taken together, these findings provide evidence that a miRNA expression signature can be developed to aid existing methods to determine the risk of recurrence for women with estrogen receptor positive breast cancers treated with endocrine therapy.

Incidental Placental Site Nodule in a Fallopian Tube

We demonstrate for the first time the imaging of unstained breast tissue biopsies using third‐harmonic generation (THG) microscopy. As a label‐free imaging technique, THG microscopy is compared to phase contrast and polarized light microscopy which are standard imaging methods for breast tissues. A simple feature detection algorithm is applied to detect tumour‐associated lymphocyte rich regions in unstained breast biopsy tissue and compared with corresponding regions identified by a pathologist from bright‐field images of hematoxylin and eosin stained breast tissue. Our results suggest that THG imaging holds potential as a complementary technique for analysing breast tissue biopsies.

Lack of APC somatic mutation is associated with early-onset colorectal cancer in African Americans

A placental site nodule is a benign proliferation of intermediate trophoblasts from a previous gestation that failed to completely involute. It is a rare entity that is often asymptomatic and is usually found incidentally weeks or even years after the pregnancy. The most common location for placental site nodules is in the uterus within the endometrium and occasionally in the cervix, diagnosed by uterine curettings or hysterectomy. However, rare extrauterine cases have been documented and should be considered as a differential diagnosis when encountered in locations such as the fallopian tube. Here, we present a case of a 28-year-old woman with a history of spontaneous abortions who was found to have a placental site nodule of the fallopian tube after postpartum tubal ligation.