Next-Generation Sequencing Pinpoints Multiple Mutations

Lara C. Pullen, PhD

September 09, 2014

CHICAGO — A typical cytology specimen contains sufficient DNA for next-generation sequencing, report researchers who suggest the tiny tissue samples should be routinely tested.

Cytology specimens, such as fine-needle aspiration (FNA) samples, commonly used for diagnosing primary and metastatic cancers, are typically tested for 1 biomarker at a time, lead investigator Christopher Hartley, MD, from Dartmouth-Hitchcock Medical Center in Lebanon, New Hampshire, explained to Medscape Medical News.

Unfortunately, cytology samples tend to contain small amounts of tissue and DNA and are inadequate for sequential testing. Next-generation sequencing allows for simultaneous analysis of multiple genes and is a much better use of limited tissue, he noted.

"Next-generation sequencing is really the only solution to having all of these different mutations that you are looking for with targeted therapies," Dr. Hartley said. His poster was among the top 5 junior member abstract winners here at the College of American Pathologists (CAP) 2014 meeting.

This is a huge thing, of course, for oncology. Dr. Philip Cagle

Dr. Hartley summarized the results from 69 consecutive next-generation sequencing reports from diagnostic cytology specimens. The samples are first placed in formalin-fixed, paraffin-embedded cell blocks. The DNA is then extracted from these and used for sequencing. The study was designed to determine the percentage of diagnostic cytology specimens that were sufficient for mutation analysis.

Dr. Hartley reported that 94% of formalin-fixed, paraffin-embedded cell blocks were adequate for sequencing. In other words, in most cases, all of the genetic tests could be run on a very limited single sample.

"This is a huge thing, of course, for oncology," Philip Cagle, MD, editor-in-chief of Archives of Pathology & Laboratory Medicine told Medscape Medical News. As treating doctors seek to minimize and focus the type of treatments, they turn to pathologists for guidance. As a result, pathologists are exploring the best way to use next-generation approaches to influence patient treatment.

Currently, next-generation sequencing is most often performed on cytology specimens diagnostic of adenocarcinoma or poorly differentiated carcinoma of the lung. This is reflected in the samples evaluated by Dr. Harley, 62% of which were endobronchial ultrasound-guided FNAs.

Table. Adequacy of Cytology Specimen for Sequencing

Specimen Total, n Adequate, n (%)
Endobronchial ultrasound-guided FNA sample 43 40 (93)
Fluid 13 13 (100)
Computed tomography–guided FNA sample 5 4 (80)
Endoscopic ultrasound–guided FNA sample 4 4 (100)
Brushings or washings 2 2 (100)
Bronchoalveolar lavage 2 2 (100)
Total 69 65 (94)


"We were surprised at how well it worked," Dr. Hartley admitted.

Molecular medicine and genomics are being highlighted as trends in pathology here at CAP. A special scientific track is dedicated to the topic as well as several courses to update pathologists on the latest guidance for molecular testing.

Sunday's session, "Molecular Medicine — Can We Afford It?" was packed to overflowing. Pathologists filled all of the seats in the large ballroom and stood at the back of the room as 3 national thought leaders discussed how genomic and molecular testing fit into both traditional and new health economic models.

"We are thinking beyond the pathology world to see how what we do improves and affects other things that physicians do," Debra Leonard, MD, PhD, from the University of Vermont College of Medicine in Burlington, told Medscape Medical News. Pathologists are sensitive to their position on the front line of determining the economic implications of molecular medicine for the patient, laboratory, and healthcare system.

Dr. Hartley and Dr. Cagle have disclosed no relevant financial relationships.

College of American Pathologists (CAP) 2014: Abstract 42. Presented September 8, 2014.


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