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Discriminating metastasised from non-metastasised seminoma based on transcriptional changes in primary tumours using NGS
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Discriminating metastasised from non-metastasised seminoma based on transcriptional changes in primary tumours using NGS
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Journal Article
Discriminating metastasised from non-metastasised seminoma based on transcriptional changes in primary tumours using NGS
2014
Overview
Background:
We aimed to better discriminate (occult) metastasised from non-metastasised seminoma based on transcriptional changes of small RNAs in the primary tumour.
Methods:
Total RNAs including small RNAs were isolated from five testicular tumours of each, lymphogenic, occult and non-metastasised patients. Next-generation sequencing (SOLID, Life Technologies) was used to examine transcriptional changes. Small RNAs showing ⩾50 reads and a significant ⩾2-fold difference using non-metastasised tumours as the reference group were examined in univariate logistic regression analysis and combinations of two small RNAs were further examined using support vector machines.
Results:
On average, 1.3 × 10
7
, 1.4 × 10
7
and 1.7 × 10
7
small RNA reads were detectable in non-metastasised, occult and lymphogenic metastasised seminoma, respectively, of which 30–32% remained after trimming. Between 59 and 68% represented annotated reads and between 8.6 and 11% were annotated small RNA tags. Of them, 137 small RNAs showed>50 reads and a two-fold difference to the reference. In univariate analysis, 32–38 small RNAs significantly discriminated lymphogenic/occult from non-metastasised seminoma, and among these different comparisons, it were the same small RNAs in 51–88%. Many combinations of two of these small RNAs allowed a complete discrimination of metastasised from non-metastasised seminoma irrespective of the metastasis subtype.
Conclusions:
Metastasised and non-metastasised seminoma can be completely discriminated with a combination of two small RNAs.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ Adult
/ Biological and medical sciences
/ Biomedical and Life Sciences
/ Cancer
/ High-Throughput Nucleotide Sequencing
/ Humans
/ Male
/ Molecular Sequence Annotation
/ Multiple tumors. Solid tumors. Tumors in childhood (general aspects)
/ Oncology
/ Testicular Neoplasms - diagnosis
/ Testicular Neoplasms - metabolism
/ Testicular Neoplasms - pathology
/ Tumors
/ Urology
