Improving Genetic Profiling from Cytology Samples
Author Information
Author(s): Kim David, Vanderbilt Chad M., Yang Soo-Ryum, Nandakumar Subhiksha, Nafa Khedoudja, Feratovic Rusmir, Rekhtman Natasha, Rijo Ivelise, Casanova Jacklyn, Yun Anita, Brannon A. Rose, Berger Michael F., Ladanyi Marc, Lin Oscar, Arcila Maria E.
Primary Institution: Memorial Sloan Kettering Cancer Center
Hypothesis
Can cytology samples be optimized for effective genetic profiling in cancer patients?
Conclusion
Cytology samples can achieve high success rates in genetic profiling, comparable to surgical samples, with proper optimization.
Supporting Evidence
- Success rates for cytology samples reached up to 93% with full optimization.
- ScfDNA testing was successful in 71% of cases where tumor tissue was depleted.
- Contamination rates were significantly lower in ScfDNA samples compared to cell block samples.
- Overall, 81% of cytology samples were successfully tested.
- High optimization of sample handling led to increased DNA recovery.
- 93.8% of successfully sequenced cases had at least one somatic alteration.
- 65% of cases had at least one targetable alteration.
Takeaway
Doctors can use small samples from patients to find important genetic information about their cancer, just like they do with bigger samples.
Methodology
The study involved optimizing cytology sample processing and analyzing 4871 samples using next-generation sequencing.
Potential Biases
Potential for cross-contamination during sample processing.
Limitations
Some cytology samples had low DNA yield and contamination issues.
Participant Demographics
{"total_patients":4633,"female_percentage":54,"male_percentage":46,"age_median":66}
Statistical Information
P-Value
p<0.05
Confidence Interval
95% CI: 11.9–12.7
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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