Biopsy misidentification identified by DNA profiling in a large multicenter trial

Molecular Auditing: An Evaluation of Unsuspected Tissue Specimen Misidentification

CONTEXT.—

Specimen misidentification is the most significant error in laboratory medicine, potentially accounting for hundreds of millions of dollars in extra health care expenses and significant morbidity in patient populations in the United States alone. New technology allows the unequivocal documentation of specimen misidentification or contamination; however, the value of this technology currently depends on suspicion of the specimen integrity by a pathologist or other health care worker.

OBJECTIVE.—

To test the hypothesis that there is a detectable incidence of unsuspected tissue specimen misidentification among cases submitted for routine surgical pathology examination.

DESIGN.—

To test this hypothesis, we selected specimen pairs that were obtained at different times and/or different hospitals from the same patient, and compared their genotypes using standardized microsatellite markers used commonly for forensic human DNA comparison in order to identify unsuspected mismatches between the specimen pairs as a trial of "molecular auditing." We preferentially selected gastrointestinal, prostate, and skin biopsies because we estimated that these types of specimens had the greatest potential for misidentification.

RESULTS.—

Of 972 specimen pairs, 1 showed an unexpected discordant genotype profile, indicating that 1 of the 2 specimens was misidentified. To date, we are unable to identify the etiology of the discordance.

CONCLUSIONS.—

These results demonstrate that, indeed, there is a low level of unsuspected tissue specimen misidentification, even in an environment with careful adherence to stringent quality assurance practices. This study demonstrates that molecular auditing of random, routine biopsy specimens can identify occult misidentified specimens, and may function as a useful quality indicator.

Specimen Provenance Testing Identifies Contamination That Affects Molecular Prognostic Assay Results in Prostate Cancer Biopsy Specimens

OBJECTIVE

To determine if tissue contamination in histologic specimens can significantly affect the results of prognostic molecular markers that are routinely used as confirmatory tests to safely assign appropriate candidates to prostate cancer active surveillance protocols.

MATERIALS AND METHODS

This study evaluates 2134 cases from a single, large urology practice that were successfully tested for DNA specimen provenance verification using short tandem repeat analysis for the presence of a significant level of contaminating DNA. After removal of the contamination, 5 of the samples were retested, and the results of the molecular diagnostic test were compared.

RESULTS

Forty-nine of the 2134 cases (2.3%) sent for DNA provenance analysis were found to possess significant levels of contamination. Of these 49 cases, 7 were resent for a repeat molecular diagnostic test after being decontaminated. Five of these prostate cancer specimens had sufficient tissue and RNA to give a more accurate cell cycle progression (CCP) score. The average absolute change in these patients' CCP scores was 0.48, with a minimum of 0.1-unit and a maximum of 1.0-unit difference. These changes in CCP scores are significant enough to cause meaningful alterations in a patient's calculated 10-year mortality rate, as defined by their combined risk score.

CONCLUSION

DNA contamination in unstained tissue sections sent for prognostic prostate cancer molecular diagnostic testing occurs in 2.3% of the cases, and can be of a magnitude that affects the results and subsequent clinical decision of appropriateness for active surveillance.

Haplotype Counting for Sensitive Chimerism Testing: Potential for Early Leukemia Relapse Detection

Fields of forensics, transplantation, and paternity rely on human identity testing. Currently, this is accomplished through amplification of microsatellites followed by capillary electrophoresis. An alternative and theoretically better approach uses multiple single-nucleotide polymorphisms located within a small region of DNA, a method we initially developed using HLA-A and called haplotype counting. Herein, we validated seven additional polymorphic loci, sequenced a total of 45 individuals from three of the 1000 Genomes populations (15 from each), and determined the number of haplotypes, heterozygosity, and polymorphic information content for each locus. In addition, we developed a multiplex PCR that amplifies five of these loci simultaneously. Using this strategy with a small cohort of leukemic patients who underwent allogeneic bone marrow transplantation, we first attempted to define a threshold (0.26% recipient) by examining seven patients who tested all donor and did not relapse. Although this initial threshold will need to be confirmed in a larger cohort, we detected increased recipient DNA above this threshold 90 to 145 days earlier than microsatellite positivity, and 127 to 142 days before clinical relapse in four of eight patients (50%). Haplotype counting using these novel loci may be useful for ultrasensitive detection in fields such as bone marrow transplantation, solid organ transplant rejection, patient identification, and forensics.

Occult Specimen Contamination in Routine Clinical Next-Generation Sequencing Testing

OBJECTIVES

To evaluate the extent of human-to-human specimen contamination in clinical next-generation sequencing (NGS) data.

METHODS

Using haplotype analysis to detect specimen admixture, with orthogonal validation by short tandem repeat analysis, we determined the rate of clinically significant (>5%) DNA contamination in clinical NGS data from 296 consecutive cases. Haplotype analysis was performed using read haplotypes at common, closely spaced single-nucleotide polymorphisms in low linkage disequilibrium in the population, which were present in regions targeted by the clinical assay. Percent admixture was estimated based on frequencies of the read haplotypes at loci that showed evidence for contamination.

RESULTS

We identified nine (3%) cases with at least 5% DNA admixture. Three cases were bone marrow transplant patients known to be chimeric. Six admixed cases were incidents of contamination, and the rate of contamination was strongly correlated with DNA yield from the tissue specimen.

CONCLUSIONS

Human-human specimen contamination occurs in clinical NGS testing. Tools for detecting contamination in NGS sequence data should be integrated into clinical bioinformatics pipelines, especially as laboratories trend toward using smaller amounts of input DNA and reporting lower frequency variants. This study provides one estimate of the rate of clinically significant human-human specimen contamination in clinical NGS testing.

The clinical and economic implications of specimen provenance complications in diagnostic prostate biopsies

PURPOSE

Inaccurate diagnoses of prostate cancer can result from transposition or contamination of patient biopsy specimens, which are known as specimen provenance complications. We assessed the clinical and economic burden of specimen provenance complications in prostate biopsies in the United States.

MATERIALS AND METHODS

We performed a comprehensive, systematic review of the literature to approximate the effect of specimen provenance complications on direct medical costs, patient QALYs and medicolegal costs. Data were extracted from published studies on specimen provenance complications rates, prostate cancer treatment efficacy, treatment cost, litigation/settlement costs after false diagnoses of prostate biopsies and patient quality of life. Sensitivity analysis was done to identify factors that most influenced the outcomes and assess the robustness of the findings.

RESULTS

Of the estimated 806,251 primary and secondary prostate biopsies performed annually in the United States 20,322 specimen provenance complications were projected to result in 4,570 clinically meaningful false diagnoses and an expected loss of 634 QALYs. The total burden of specimen provenance complications was projected to exceed $879.9 million or $3,776 per positive cancer diagnosis. This estimate was most sensitive to the indemnity cost per false-positive case and the rate of transpositions at independent reference laboratories.

CONCLUSIONS

The societal burden of specimen provenance complications in patients who undergo prostate biopsy exceeds $880 million annually in the United States. This analysis framework may be useful as policy makers, health organizations and researchers seek to decrease false diagnoses of prostate cancer and the consequent effects of delayed or unnecessary treatment. Further study is warranted to quantify the economic burden among additional diseases.

Radiofrequency identification specimen tracking in anatomical pathology: pilot study of 1067 consecutive prostate biopsies

Improved methods such as radiofrequency identification (RFID) are needed to optimize specimen tracking in anatomical pathology. We undertook a study of RFID in an effort to optimize specimen tracking and patient identification, including the following: (1) creation of workflow process maps, (2) evaluation of existing RFID hardware technologies, (3) creation of Web-based software to support the RFID-enabled workflow, and (4) assessment of the impact with a series of prostate biopsies. We identified multiple steps in the workflow process in which RFID enhanced specimen tracking. Multiple product choices were found that could withstand the harsh heat and chemical environments encountered in pathology processing, and software that was compatible with our laboratory information system was designed in-house. A total of 1067 prostate biopsies were received, and 78.3% were successfully processed with the RFID system. Radiofrequency identification allowed dynamic specimen tracking throughout the workflow process in anatomical pathology.

Rate of occult specimen provenance complications in routine clinical practice

Occult specimen provenance complications (SPCs), which occur when there is an absence of any direct or indirect indication that a specimen switch or contamination may have occurred, constitute a significant patient safety and medical-legal problem because they can lead to misdiagnosis. However, the rate at which occult SPCs occur is unknown because, by definition, this category of errors is not identified by standard laboratory practices. In this study, we evaluated a data set comprising almost 13,000 prostate biopsies that were prospectively tested for specimen provenance errors as part of routine clinical practice. The frequency of occult type 1 errors (a complete transposition between patients) and type 2 errors (contamination of the patient's tissue with 1 or more unrelated patients) was 0.26% and 0.67%, respectively; every urology practice setting and surgical pathology laboratory type with a representative sample size experienced at least 1 type 1 and 1 type 2 error during the study period. Overall, the mean frequency of SPCs across practice settings was 0.22% for type 1 errors and 1.69% for type 2 errors. The type 1 rate showed no correlation with a surgical pathology laboratory setting or urologic practice group setting; the type 2 rate correlated solely with a surgical pathology laboratory setting. The occult SPC rate in this limited data set provides an estimate of the scope of the problem of potential misdiagnosis as a result of occult specimen provenance errors in routine clinical practice.

Markers for screening lynch syndrome are reliable and useful for identifying the specimen mislabeling

Background

During specimen processing in surgical pathology laboratories, specimen-related adverse events (SRAEs), such as mislabeling and specimen mixed-up might occur. In these situations, molecular techniques using short tandem repeat (STR) loci are required to identify the personal identity. Microsatellite instability (MSI) test is widely used for screening the hereditary non-polyposis colon cancer (Lynch syndrome) in surgical pathologies using polymorphic STR markers. We tried to evaluate the applicability of the MSI test for SRAEs.

Methods

We obtained 253 MSI test results to analyze the allele frequencies. After calibrating the estimated nucleotide lengths, we calculated the allele frequencies, a random match probability, and a likelihood ratio (LR) of three dinucleotide STR markers (D5S349, D17S250, and D2S123).

Results

The distribution of LR was 136.38 to 5,606,213.10. There was no case of LR<100. In addition, there were 153 cases (60.5%) of LR ranging from 100 to 10,000 and 100 cases (39.5%) of LR>10,000. Furthermore, the combined probability of identity was 9.23×10^-4 and the combined power of exclusion was 0.99908.

Conclusions

Using the three STR markers that are recommended for MSI test, all the cases were positively identified in 1% range and about one-third cases showed high LR (>10,000). These results showed that MSI tests are useful to screen the personal identity in case of SRAE in pathology laboratories.

Usefulness of prostate-specific antigen (PSA) rise as a marker of prostate cancer in men treated with dutasteride: lessons from the REDUCE study

OBJECTIVES

To determine if dutasteride-treated men can be monitored safely and adequately for prostate cancer based on data from the Reduction by Dutasteride in Prostate Cancer Events (REDUCE) study. To analyse whether the use of treatment-specific criteria for repeat biopsy maintains the usefulness of prostate-specific antigen (PSA) level for detecting high grade cancers.

PATIENTS AND METHODS

The REDUCE study was a randomized, double-blind, placebo-controlled investigation of whether dutasteride (0.5 mg/day) reduced the risk of biopsy-detectable prostate cancer in men with a previous negative biopsy. The usefulness of PSA was evaluated using biopsy thresholds defined by National Comprehensive Cancer Network guidelines in the placebo group and any rise in PSA from nadir (the lowest PSA level achieved while in the study) in the dutasteride group. The number of cancers detected on biopsy in the absence of increased/suspicious PSA level as well as sensitivity, specificity, positive predictive value and negative predictive value for high grade prostate cancer detection were analysed by treatment group. Prostate cancer pathological characteristics were compared between men who did and did not meet biopsy thresholds.

RESULTS

Of 8231 men randomized, 3305 (dutasteride) and 3424 (placebo) underwent at least one prostate biopsy during the study and were included in the analysis. If only men meeting biopsy thresholds underwent biopsy, 25% (47/191) of Gleason 7 and 24% (7/29) of Gleason 8-10 cancers would have been missed in the dutasteride group, and 37% (78/209) of Gleason 7 and 22% (4/18) Gleason 8-10 cancers would have been missed in the placebo group. In both groups, the incidence of Gleason 7 and Gleason 8-10 cancers generally increased with greater rises in PSA. Sensitivity of PSA kinetics was higher and specificity was lower for the detection of Gleason 7-10 cancers in men treated with dutasteride vs placebo. Men with Gleason 7 and Gleason 8-10 cancer meeting biopsy thresholds had greater numbers of positive cores, percent core involvement, and biopsy cancer volume vs men not meeting thresholds.

CONCLUSION

Using treatment-specific biopsy thresholds, the present study shows that the ability of PSA kinetics to detect high grade prostate cancer is maintained with dutasteride compared with placebo in men with a previous negative biopsy. The sensitivity of PSA kinetics with dutasteride was similar to (Gleason 8-10) or higher than (Gleason 7-10) the placebo group; however, biopsy decisions based on a single increased PSA measurement from nadir in the dutasteride group resulted in a lower specificity compared with using a comparable biopsy threshold in the placebo group, indicating the importance of confirmation of PSA measurements.