The use of high throughput sequencing (HTS) technologies in biomedicine is expanding in a variety of fields in recent years. The 454 system is an HTS platform that is ideally suited to characterize B cell receptor (BCR) repertoires by sequencing of immunoglobulin (Ig) genes, as it is able to sequence stretches of several hundred nucleotides. Most studies that used this platform for antibody repertoire analyses have started from fresh or frozen tissues or peripheral blood samples, and rely on starting with optimal quality DNA. In this paper we demonstrate that BCR repertoire analysis can be done using DNA from formalin-fixed paraffin-embedded (FFPE) human tissue samples. The heterogeneity of BCR repertoires we obtained confirms the plausibility of HTS of DNA from FFPE specimens. The establishment of experimental protocols and computational tools that enable sequence data analysis from the low quality DNA of FFPE tissues is important for enabling research, as it would enable the use of the rich source of preserved samples in clinical biobanks and biopsy archives.
Bibliographical noteFunding Information:
This work was supported in parts by the Israel Science Foundation (grant number 270/09 ), a grant from the Israel Cancer Association (to RM and IB), a grant from the Israel Cancer Association USA (to IB) and a Human Frontiers Science Program Research Grant (to RM and DDW). The funding sources had no role in the study design, in the collection, analysis and interpretation of data, in the writing of the report, or in the decision to submit the article for publication. The work was included in MM's studies towards the MSc degree in Bar-Ilan University, and she was supported by a Combined Technologies Scholarship from the Israeli Council for Higher Education. The work was also included in ARS and NAR's studies towards the MSc degree in Bar-Ilan University.
- FFPE tissues
- Formalin-fixed paraffin-embedded tissues
- High throughput sequencing
- Ig variable region genes