Pathology in the era of "Personalized Medicine": The need to learn how to integrate multivariate immunohistochemical and "omics" data with clinicopathologic information in a clinically relevant way"

"Personalized medicine" has been proposed as a new paradigm for patient care that, based on the integration of genomics and other "omics" data with clinical and other multidisciplinary information, promises early disease detection, improved outcomes and reduced side effects to therapies. Pathologists have become important participants in this new approach as the guardians of tissues and experts in the performance of molecular and other laboratory tests. Large amounts of new laboratory data in multiple neoplasms and other entities are being reported but there has been limited discussion about how best to evaluate the clinical significance of this information and how to integrate it into currently available diagnostic and therapeutic modalities. This article introduces a variety of epistemological problems presented by the "personalized medicine" paradigm and briefly discusses various topics that will be evaluated in further detail in future articles of this new series on Evidence-Based Pathology.

The Power of Proficiency Testing: Unraveling Single-Nucleotide Polymorphism Interference, With Potential Impact on Clinical Testing of Spinocerebellar Ataxia Type 3

CONTEXT.—

The College of American Pathologists proficiency testing program has been instrumental in identifying problems in clinical testing.

OBJECTIVE.—

To describe how this program was used to identify a single-nucleotide polymorphism that affects clinical testing for spinocerebellar ataxia type 3.

DESIGN.—

A proficiency testing sample with discordant results for spinocerebellar ataxia type 3 analysis was further evaluated by targeted Sanger sequencing and genotype polymerase chain reaction using multiple DNA polymerases.

RESULTS.—

Of 28 laboratories responding in the spinocerebellar ataxia type 3 Proficiency Survey, 18 reported an incorrect homozygous result and 10 reported the expected heterozygous result. A heterozygous single-nucleotide polymorphism complementary to the 3' end of a published forward primer was identified in the proficiency testing sample, which may have led to allele dropout. However, this primer was used by only 3 of 18 laboratories (16%) reporting a homozygous result. A new forward primer of identical sequence, except for the 3' end being complementary to the single-nucleotide polymorphism, showed the expected heterozygous pattern. The possibility of DNA polymerase 3'-5' exonuclease activity contributing to allele dropout was investigated by testing 9 additional polymerases with and without exonuclease activity. No clear pattern emerged, but enzymes with and without 3'-5' exonuclease activity yielded both homozygous and expected heterozygous results with the published forward primer.

CONCLUSIONS.—

Proactive systematic primer sequence checking is recommended because single-nucleotide polymorphism interference may result in allele dropout and impact clinical testing. Allele dropout is also influenced by other factors, including DNA polymerase exonuclease activity.

Development of a pilot proficiency program for human papillomavirus DNA detection

Human papillomavirus (HPV) DNA testing has become routine in many diagnostic laboratories, particularly with changes from cervical cytology to HPV DNA as primary screening as of 1 December 2017 in Australia. External quality assurance (EQA) is essential for assessment of laboratory performance once HPV testing is implemented. The aim of this study was to develop a pilot program to evaluate and determine stability of material that could be utilised in an ongoing external quality assurance program (EQAP). Two sample types were evaluated: cells in PreservCyt solution (ThinPrep) from stored clinical specimens and HPV-seeded swabs. Two panels sent 5 months apart were distributed to 18 Australian and two New Zealand laboratories (participants) for testing by Hybrid Capture 2 (HC2) or alternative molecular methods. Participants were given 1 month to test specimens. Eight ThinPrep specimens in Panel 1 were reported correctly by 73% (11/15) of HC2 participants and 40% (2/5) of participants performing alternative methods. Of eight dry swab specimens, 58% (23/40) and 78% (25/32) were correctly identified by HC2 and alternative methods, respectively. Panel 2 included four ThinPrep and two swab specimens. ThinPrep specimens were reported correctly by 100% (60/60) of participants utilising HC2 and 95% (19/20) utilising alternative methods. Dry swab specimens were reported correctly by 89% (25/28) of participants utilising HC2 and 100% (10/10) of participants utilising alternative methods. These results indicate that both specimen types are suitable for utilisation in an EQAP and outline some issues of EQAP for ongoing assessment of HPV molecular methods in diagnostic molecular laboratories.

Performance of Roche cobas high-risk human papillomavirus (hrHPV) testing in the two most common liquid-based Papanicolaou test platforms

INTRODUCTION

High-risk human papillomavirus (hrHPV) testing is important in cervical cancer screening and management algorithms. Roche (Pleasanton, Calif.) cobas hrHPV testing is commonly performed on both ThinPrep (TP) and SurePath (SP) samples, but performance of these platforms has not been fully investigated in the literature.

MATERIALS AND METHODS

Roche hrHPV testing was performed on 47,885 (TP = 18,295; SP = 29,590) out of 130,648 consecutive Papanicolaou tests, over 16 months; 1895 of those had interpretable biopsies.

RESULTS

The overall hrHPV detection rates were similar in TP (13.5%) and SP (13.1%). The hrHPV positive rate was higher in SP (8.5%) than TP (7.3%, P < 0.0001) in women with negative cytology; the difference in other cytologic diagnosis categories was insignificant. TP samples had significantly fewer negative cytology diagnoses (7.3% versus 8.5%, P < 0.0001), more low-grade abnormalities in cytology and biopsies, and higher colposcopy referral rate (4.8% versus 2.7%, P < 0.0001) than SP. There were no differences between TP and SP in detecting ≥HSIL by hrHPV testing, cytology or biopsy. SP samples had a significantly higher rate of HPV 16/18 but a lower rate of non-16/18 hrHPV genotypes than TP.

CONCLUSIONS

Roche cobas hrHPV testing was similar in both TP and SP platforms. The significantly lower hrHPV detection rate in cytological negative TP samples is likely related to higher cytology reporting rates for indeterminate and low-grade diagnoses in TP than SP samples. Significant differences were also observed in hrHPV genotyping results between TP and SP. Clinical risk stratification based on hrHPV testing may need to take testing platforms into consideration.

Update on the College of American Pathologists Experience With High-Risk Human Papillomavirus Proficiency Testing for Cytology

Context.—

Since 2008, the College of American Pathologists has provided the human papillomavirus for cytology laboratories (CHPV) proficiency testing program to help laboratories meet the requirements of the Clinical Laboratory Improvement Amendments of 1988.

Objectives.—

To provide an update on trends in proficiency testing performance in the College of American Pathologists CHPV program during the 4-year period from 2011 through 2014 and to compare those trends with the preceding first 3 years of the program.

Design.—

Responses of laboratories participating in the CHPV program from 2011 through 2014 were analyzed using a nonlinear mixed model to compare different combinations of testing medium and platform.

Results.—

In total, 818 laboratories participated in the CHPV program at least once during the 4 years, with participation increasing during the study period. Concordance of participant responses with the target result was more than 98% (38 280 of 38 892). Overall performance with all 3 testing media—ThinPrep (Hologic, Bedford, Massachusetts), SurePath (Becton, Dickinson and Company, Franklin Lakes, New Jersey), or Digene (Qiagen, Valencia, California)—was equivalent (P = .51), and all 4 US Food and Drug Administration (FDA)–approved platforms—Hybrid Capture 2 (Qiagen), Cervista (Hologic), Aptima (Hologic), and cobas (Roche Molecular Systems, Pleasanton, California)—outperformed laboratory-developed tests, unspecified commercial kits, and other (noncommercial) methods in ThinPrep medium (P &lt; .001). However, certain off-label combinations of platform and medium, most notably Cervista with SurePath, demonstrated suboptimal performance (P &lt; .001).

Conclusions.—

Laboratories demonstrated proficiency in using various combinations of testing media and platforms offered in the CHPV program, with statistically significant performance differences in certain combinations. These observations may be relevant in the current discussions about FDA oversight of laboratory-developed tests.

Clinical Performance of Hybrid Capture 2 Human Papillomavirus Testing for Recurrent High-Grade Cervical/Vaginal Intraepithelial Neoplasm in Patients With an ASC-US Papanicolaou Test Result During Long-Term Posttherapy Follow-up Monitoring

Context

Women who have been treated for high-grade cervical or vaginal intraepithelial neoplasia (CIN or VAIN) or invasive carcinoma are at risk for recurrent/persistent disease and require long-term monitoring. The role of human papillomavirus (HPV) testing in this setting is unclear.

Objective

To evaluate the clinical performance of the Hybrid Capture 2 (HC2) HPV test for recurrent/residual high-grade CIN or VAIN in patients with a posttherapy abnormal squamous cells of undetermined significance (ASC-US) Papanicolaou test result.

Design

We reviewed the follow-up data on 100 patients who had an ASC-US Papanicolaou test and HC2 HPV results after treatment for high-grade CIN/VAIN or carcinoma. Human papillomavirus genotyping was performed for women with a negative HC2 result whose follow-up biopsy revealed CIN/VAIN 2+.

Results

The patients' mean age was 47 years. The HC2 test result was positive in 33% of the patients. Follow-up biopsy was available for 17 of these patients (52%) and for 25 of the 67 patients (37%) with a negative HC2 result. A total of 5 of the patients (29%) with a positive HC2 result and 2 of the patients (8%) with a negative HC2 result had CIN/VAIN 3 on follow-up biopsy, a statistically insignificant difference (P = .10). Human papillomavirus 16/18 genotypes were detected in the CIN/VAIN 2+ lesions of 5 patients with a negative HC2 result.

Conclusion

HC2 yielded a false-negative rate of 8% for CIN 3. HC2 testing therefore may not be sufficient for triage of patients with an ASC-US Papanicolaou test result. Patients with ASC-US during long-term posttherapy follow-up need close monitoring, with colposcopic evaluation if clinically indicated.