title: Analysis of Mutational Hotspots in Routinely Processed Bone Marrow Trephines by Pyrosequencing®.
abstract: Formalin-fixed, paraffin-embedded (FFPE) bone marrow trephines are widely used in pathology, because they best preserve the morphological details of the bone marrow. However, DNA isolated from FFPE material is fragmented, limiting the size of amplification products, which is a challenge for all sequencing applications.Pyrosequencing(®) is a quantitative and sensitive method for the detection of single-nucleotide variations (SNVs) in DNA samples. Pyrosequencing can easily be performed in a 96-well-plate format with a cost-effective medium-sized throughput.This chapter provides a general outline of SNV detection in FFPE bone marrow trephines, including a detailed protocol of the Pyrosequencing procedure and guidelines for the design of new assays and evaluation of Pyrograms. The strengths of this approach are discussed using myeloproliferative neoplasms as an example.
authors.affiliation: Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Bartels
authors.forename: Ulrich
authors.initials: U
authors.lastname: Lehmann
mesh_terms: D053000:Analytic Sample Preparation Methods; D001853:Bone Marrow / Q000378:metabolism*; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D018572:Disease-Free Survival; D006801:Humans; D007938:Leukemia / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D016133:Polymerase Chain Reaction; D055728:Primary Myelofibrosis / Q000235:genetics; D012261:Ribonucleoproteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D000068103:Serine-Arginine Splicing Factors; D013922:Thrombocytosis / Q000235:genetics; D016707:Tissue Fixation
chemical_list: D009687:Nuclear Proteins; D012261:Ribonucleoproteins; C073288:SRSF2 protein, human; D000068103:Serine-Arginine Splicing Factors; D004247:DNA