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Molecular Diagnostics of Chronic Myeloid Leukemia: Precision Medicine via Gold Nanoparticles
Published in Il-Jin Kim, Companion Diagnostics (CDx) in Precision Medicine, 2019
Raquel Vinhas, Alexandra R. Fernandes, Pedro V. Baptista
Mutational analysis is also recommended upon therapy failure. In fact, approximately 30% of CML patients fail to respond to imatinib, whose major mechanism of resistance is associated to ab initio or acquired mutations within the BCR-ABL1 kinase domain that affect imatinib binding.20, 42–46 Mutation screening is currently done via Sanger or next-generation sequencing, which are capable to detect a point mutation even if the mutated clone accounts for only 10% of all Ph+ cells.47 Other groundbreaking methodologies include extremely sensitive techniques, such as mass spectrometry, ultra-deep sequencing, pyrosequencing, denaturing high-performance liquid chromatography, double-gradient denaturing electrophoresis, multiplex-PCR, or allele-specific oligonucleotide PCR.11
Precision medicine in ovarian carcinoma
Published in Debmalya Barh, Precision Medicine in Cancers and Non-Communicable Diseases, 2018
Shailendra Dwivedi, Purvi Purohit, Radhieka Misra, Jeewan Ram Vishnoi, Apul Goel, Puneet Pareek, Sanjay Khattri, Praveen Sharma, Sanjeev Misra, Kamlesh Kumar Pant
The chromatographic screening of polymorphic changes of disease-causing mutations by utilizing denaturing high-performance liquid chromatography (DHPLC) is one of the novel technologies that occurred. DHPLC discloses the existence of a genetic variation by the differential retention of homo- and heteroduplex DNA on reversed-phase chromatography under partial denaturation. Single-base substitutions, deletions, and insertions can be identified effectively by ultraviolet (UV) or fluorescence monitoring within 2 to 3 minutes in unpurified PCR products as large as 1.5 kilobases. These characteristics, together with its low cost, make DHPLC one of the most potent techniques for mutational analysis.
Detection Techniques for Single Nucleotide Polymorphisms
Published in Attila Lorincz, Nucleic Acid Testing for Human Disease, 2016
W. Mathias Howell, Johan Stenberg, Chatarina Larsson, Mats Nilsson, Ulf Landegren
A number of methods can speed the search for such unknown sequence variants. Single-strand conformation polymorphism (SSCP),138 denaturing gradient gel electrophoresis (DGGE),139 and denaturing high performance liquid chromatography (dHPLC)140 are examples of such methods. Although these three techniques can identify DNA fragments bearing sequence differences, the position or nature of genetic change is difficult to characterize based on results of these methods alone. Therefore, these methods are combined with or in fact replaced by sequencing techniques to derive exact sequence information.
From old markers to next generation: reconstructing the history of the peopling of Sardinia
Published in Annals of Human Biology, 2021
Carla Maria Calò, Giuseppe Vona, Renato Robledo, Paolo Francalacci
With respect to Y chromosome variability, a significant improvement to our knowledge of it was due to the introduction of the Denaturing High Performance Liquid Chromatography (D-HPLC) technology, with a 10-fold increase in the number of polymorphisms available in this chromosome (Underhill et al. 2000), using a world-wide sample which included a Sardinian subsample. Using the same technology and focussing on European populations, Semino et al. (2000) showed that Sardinians have the same haplotypes of other European populations, but with a remarkable peculiarity for the frequencies of some SNPs (namely M26, which reaches the highest percentages among Europeans, and M13, of Sub-Saharan origin, not found in the other populations analysed), suggesting that the Sardinian population has been shaped during the generations through random genetic drift, amplified by demographic events such as isolation and consanguinity.
A rapid molecular diagnostic method for spinal muscular atrophy
Published in Journal of Neurogenetics, 2021
Kai-Chen Wang, Chiao-Yuan Fang, Chi-Chang Chang, Chien-Kuan Chiang, Yi-Wen Chen
Recently, carrier screening for SMA has been highly recommended by obstetrician in basic prenatal inspection because of the high carrier frequency (1/40–1/60) as well as the genetic risk of this disease. Generally, an unaffected individual has two or more copies of SMN1, SMA carrier possesses one copy which is symptom-free, and SMA patient lacks SMN1 gene. Mendel’s law states that a 25% incidence rate would be expected to inherit SMA, if both parents were SMA carriers (Figure 1). Up to date, molecular diagnosis of SMA is performed using real-time PCR, denaturing high performance liquid chromatography (DHPLC), or multiplex ligation-dependent probe amplification (MLPA) mostly. But an important limitation of the current established assays is the need for parallel-run standard curve to align with the value of unknown sample so as to obtain exact copy numbers of SMN1 and SMN2 genes.
Accuracy of self-reported family history of cancer, mutation status and tumor characteristics in patients with early onset breast cancer
Published in Acta Oncologica, 2018
Annelie Augustinsson, Carolina Ellberg, Ulf Kristoffersson, Åke Borg, Håkan Olsson
Information regarding mutation status was obtained from the OnkGen Register at Skåne University Hospital in Lund. As described in previous articles [13,14], mutation screening was originally performed using protein truncation test (PTT), single-strand conformation polymorphism (SSCP) and denaturing high-performance liquid chromatography (DHPLC). Mutations were verified by sequencing. In 31 BC patients, for whom no mutations in BRCA1 or BRCA2 were found in previous screenings, a reanalysis was performed between the years 2012 and 2015. These BC patients had been re-remitted by physicians at the Oncogenetic Clinic in Lund for further investigation due to various reasons, e.g., a new incident BC-case in the BC patient’s family, an inquiry from a relative, and/or a strong family history of cancer. The reanalysis was performed by using SureSelect (Agilent Technology, Santa Clara, CA, USA) and included the genes BRCA1, BRCA2, TP53, PTEN, CDH1, STK11, CHEK2, PALB2, RAD51C and RAD51D. Blood samples were sequenced using either Genome Analyzer II or Hiseq 2500 (Illumina, San Diego, CA, USA). Alignment was made with Novoalign and variants were detected with Unified Genotyper, GATK. Complementary Sanger sequencing was performed on all fragments/exons that did not have acceptable coverage.