Relevant bibliographies by topics / Molecular inversion probe (MIP)

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Academic literature on the topic 'Molecular inversion probe (MIP)'

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Published: 4 June 2021
Last updated: 3 February 2022

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Journal articles on the topic "Molecular inversion probe (MIP)"

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Wang, Y. "Allele quantification using molecular inversion probes (MIP)." Nucleic Acids Research 33, no. 21 (November 27, 2005): e183-e183. http://dx.doi.org/10.1093/nar/gni177.

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Schiffman, J. D., K. M. Welch, R. Davis, G. V. Dahl, N. J. Lacayo, M. Faham, J. M. Ford, and H. Ji. "Adapting molecular inversion probe (MIP) technology for allele quantification in childhood leukemia." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 9530. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.9530.

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9530 Background: Leukemia accounts for ∼40% of newly diagnosed pediatric malignancies, and relapsed leukemia is the leading cause of death in childhood cancer. Genomic instability events contribute to neoplastic development and have been used to classify and risk stratify non-leukemic adult and pediatric tumors. Analyzing leukemic blasts for gene copy changes with advanced molecular techniques could prove useful in further risk stratifying and developing new treatment strategies for pediatric leukemia. Methods: Molecular Inversion Probes (MIPs) analyze genetic target sequences in parallel with high specificity and sensitivity at the highest genomic resolution, and were originally designed for single nucleotide genotyping. The MIP assay was adapted to analyze both gene copy number and loss of heterozygosity (LOH) events in pediatric leukemia samples (pre-B ALL, T-ALL, AML). DNA was extracted (100 ng) from paired bone marrow (diagnosis) and peripheral blood (remission) samples (n = 40). The MIP assay was run with a customized Affymetrix 20K Cancer Panel (representing oncogenes, tumor suppressor, DNA repair, cell growth, and metabolism genes). Gene copy number changes were identified by comparing probe signal intensity between leukemia samples and normal cell-lines. LOH events were determined by identifying genotype changes between matched leukemic and remission samples. Results: Each sample had unique patterns of multiple gene copy changes and LOH events distributed across all chromosomes. Additionally, samples were found to have overlapping copy number changes and LOH regardless of leukemia type. AML samples had fewer LOH events and could be separated by unsupervised clustering from the other leukemia samples. Conclusions: MIPs represent novel genotyping technology that can be adapted for gene copy analysis of childhood leukemia. Unique and distinguishing signatures of allelic imbalance can be determined between ALL and AML clinical samples using MIP technology. The unexpected overlap of LOH and deleted genes may represent a common molecular mechanism that requires further investigation. No significant financial relationships to disclose.
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Liu, Jingqian, Syukri Shukor, Shuxiang Li, Alfred Tamayo, Lorenzo Tosi, Benjamin Larman, Vikas Nanda, Wilma K. Olson, and Biju Parekkadan. "Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency." Biomolecules 9, no. 5 (May 22, 2019): 199. http://dx.doi.org/10.3390/biom9050199.

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Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology applications, such as long-read genome sequencing and the creation of open reading frame (ORF) libraries. Long-adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to clone long DNA fragments. LASSO probes are molecular inversion probes (MIP) engineered with an adapter region of user-defined length, flanked between template-specific probe sequences. Herein, we demonstrate that the adapter length is a key feature of LASSO that influences the efficiency of gene capture and cloning. Furthermore, we applied a model based on Monte Carlo molecular simulation in order to study the relationship between the long-adapter length of LASSO and capture enrichment. Our results suggest that the adapter length is a factor that contributes to the free energy of target–probe interaction, thereby determining the efficiency of capture. The results indicate that LASSOs with extremely long adapters cannot capture the targets well. They also suggest that targets of different lengths may prefer adapters of different lengths.
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Ji, Hanlee P., Katrina M. Welch, Yuker Wang, Malek Faham, Takashi Akasaka, Debbie Czerwinski, Ronald W. Davis, and Ronald Levy. "Gene-Specific Delineation of Copy Number Aberrations in Follicular Lymphoma with Molecular Inversion Probes." Blood 110, no. 11 (November 16, 2007): 2603. http://dx.doi.org/10.1182/blood.v110.11.2603.2603.

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Abstract Background: Follicular lymphoma, derived from germinal center B cells, is one of the most common types of lymphoma. Follicular lymphoma like many other malignancies demonstrates genomic instability, a phenomenon where tumor cells accumulate various genetic changes including point mutations, genomic deletions and gene amplifications. Such genomic aberrations may contribute to cancer phenotype such as transformation. Previous studies of follicular lymphoma have shown a combination of cytogenetic - aneuploidy type events from gross chromosomal alterations to smaller deletions and amplifications. For example, deletions in chromosome 6q may be associated with follicular lymphoma aggressiveness. Efforts to identify these changes have used traditional karyotyping, comparative genomic hybridization (CGH) or traditional genetic markers (microsatellites) for loss of heterozygosity (LOH) analysis. Characterization of of genomic instability in follicular lymphoma has not been thoroughly investigated on a genomic scale. Objectives: We have employed a novel genomic technology relying on molecular inversion probes (MIPs) to conduct a large scale analysis of gene copy aberrations in follicular lymphoma. MIPs technology enables querying any gene sequence in the genome at a high resolution for allele-specific gene copy alterations and polymorphisms simultaneously, a significant improvement over other genomic methods such as array CGH. We are using this genomic technology to delineate concordant gene copy aberrations in follicular lymphoma that may influence a variety of clinical outcomes using a probe set with over 7,000 cancer-related genes among 25,000 loci. Methods: DNA was extracted from a cohort of follicular lymphoma clinical samples obtained at the time of diagnosis and prior to treatment. B-cell lymphoma cells were purified using a Rosette purification scheme, genomic DNA was isolated from the purified tumor cell populations from 37 individual lymphoma samples and the cohort was analyzed with a MIP cancer probe set described above. Each probe contains two unique recognition sequences to a genomic DNA target and a unique barcode sequence. The molecular inversion probe assay was conducted. The final products were hybridized to a generic barcode microarray overnight and interrogated by an Affymetrix scanner. Barcode array data was preprocessed and gene copy number was extrapolated for each molecular inversion probe. Concordant gene copy aberrations were determined across the sample set. Results: Follicular lymphoma samples from pretreated patients have common patterns of chromosomal losses, gains and multiple gene deletions with large overlap in some areas of deletion. Common large scale chromosomal deletions and amplifications included regions of chromosome 6 and 18. Multiple individual genes were found to be commonly amplified or deleted as well including BTK which is suspected to play a role in follicular lymphoma. Conclusions: MIP technology has been used to analyze follicular lymphoma for highly sensitive and specific gene copy analysis. We identified concordant gene copy alterations found across the majority of samples in the cohort, suggesting that these aberrations may play a role in follicular lymphoma development. We are pursuing additional studies to confirm these findings.
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Schiffman, Joshua D., Katrina Welch, Ronald Davis, Norman J. Lacayo, Gary V. Dahl, Yuker Wang, Malek Faham, James M. Ford, and Hanlee P. Ji. "Molecular Inversion Probes (MIPs) Identify Novel Areas of Allelic Imbalance in Childhood Leukemia." Blood 110, no. 11 (November 16, 2007): 1438. http://dx.doi.org/10.1182/blood.v110.11.1438.1438.

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Abstract Background: Leukemia accounts for over 30% of newly diagnosed childhood malignancies, and is the leading cause of death for children with cancer. Genomic instability events contribute to tumorigenesis and have been used to classify and risk stratify adult and pediatric cancers. Molecular Inversion Probes (MIPs) analyze genetic target sequences in parallel at the highest genomic resolution, and can detect both gene copy number and loss of heterozygosity (LOH) events in clinical samples. Studying pediatric leukemia samples with MIP technology may identify new molecular alterations that could prove useful in risk stratification and discovery of new therapeutic targets for childhood leukemia. Objective: To use MIP technology to identify novel areas of allelic imbalance in childhood leukemia. Methods: DNA was extracted from leukemia blasts at diagnosis (n=45, 23 pre-B ALL, 14 AML, 7 pre-T ALL, 1 Burkitt’s). DNA was also extracted from normal peripheral blood collected at remission to use as paired germline controls. The MIP assay was run with a customized Affymetrix 24K Cancer Panel (representing oncogenes, tumor suppressor, DNA repair, cell growth, and metabolism genes). DNA required for this assay was limited to 75 ng per sample. Copy number changes and LOH were identified by comparing probe signal intensity between leukemia and normal germline samples. Clinical cytogenetic data (karyotype and FISH analysis) was used as a control to confirm findings from known areas of allelic imbalance. Results: Each leukemia sample had unique patterns of allelic imbalance distributed across all chromosomes. MIPs identified all clinically reported cytogenetic copy number changes for each sample, in addition to areas of allelic imbalance not clinically reported. Samples had recurring areas of copy number changes and LOH events shared by all leukemia types. MIPs detected areas of allelic imbalance in both previously described and novel genes. Areas of recurring genomic deletions included: ATR (3q23), TLX3 (5q35.1), ADRB3 (8p12), CDKN2A (9p21.3), DOCK8 (9p24.3), PAX5 (9p13.2), PTPN11 (12q24.13), C3AR1 (12p13.31), TCRA (14q11.2), AKT1 (q14q32.33). Areas of recurring genomic amplification included: SLC2A9 (4p16.1), RAI14 (5p13.2), CDH12 (5p14.3), PMCHL1(5p14.3), AURKB (17p13.1). These findings are being validated with Quantitative Real-Time PCR. Conclusions: MIPs represent a novel genomic technology that can identify previously unreported gene copy number and LOH events in childhood leukemia. Unique and overlapping areas of allelic imbalance were found in both childhood ALL and AML clinical samples. The shared genomic regions of allelic imbalance between different leukemia types may represent a common molecular mechanism of leukemogenesis that warrants further investigation. Analysis of more childhood leukemia samples through Pediatric Cooperative Groups may help to determine how common these areas of allelic imbalance are in children and whether they are of prognostic significance. Further exploration of these copy number and LOH events may help us to better understand the biology of childhood leukemia and its clinical behavior.
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Schiffman, Joshua D., Hanlee Ji, Katrina M. Welch, Ron Davis, Gary Van Houten Dahl, Norman J. Lacayo, and James M. Ford. "Novel Allele Quantification Method To Classify Childhood Leukemia." Blood 108, no. 11 (November 1, 2006): 2273. http://dx.doi.org/10.1182/blood.v108.11.2273.2273.

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Abstract Background: Leukemia is the most common pediatric malignancy, accounting for nearly 40% of all new childhood cancer. The cure rates for pediatric ALL have increased to more than 80% and the cure rates for pediatric AML now approach 50%. Much of this progress can be attributed to cytogenetic and molecular risk stratification with subsequent randomized control trials. Genomic instability events may also serve as relevant prognostic biomarkers. A novel high-throughput genomic technology called Molecular Inversion Probes (MIPs) quantifies genomic instability, gene copy number and allelic imbalances at the highest genomic resolution. MIPs can analyze genetic target sequences in parallel with high specificity and sensitivity. Further classifying leukemic blasts using more precise molecular techniques could prove useful in further risk stratifying and developing new treatment strategies. Objective: To adapt MIPs to characterize and define unique molecular subtypes of childhood leukemia. Methods: DNA was extracted from AML and ALL clinical samples obtained at diagnosis. 400 ng of leukemic DNA was mixed with a previously synthesized MIP cancer probe set (667 probes representing all human chromosomes from exon sequences of 298 cancer genes); each probe contains two unique recognition sequences to targeted genomic DNA and a unique barcode (tag) sequence. A thermostable polymerase and ligase were added, and the mixture was denatured. Probe homology sequences were then annealed to complementary genome sites. Standard PCR reagants were added including one fluorescent-labeled primer and unlabeled primer. The reaction was thermocycled and probes circularized in the nucleotide specific “gap fill” reaction were amplified. The PCR mixture was hybridized to a barcode microarray overnight. The chip was stained and washed, and then interrogated by an Affymetrix scanner via argon laser excitation at 488-nm. ‘Cluster along Chromosomes’ analysis was performed to detect significant amplifications or deletions. Results: Childhood ALL and AML samples had unique patterns of multiple gene deletions. Additionally, overlap was found in several of these deleted genes. Significantly deleted genes in common between ALL and AML samples included: RAP1GA1, HYAL1, HSPA9B, CSF1R, TNF, NOTCH4, FANCE, CCND3, BAG2, PLAGL1, MAD1L1, POLM, POLD2, IGFBP3, PSD, SUFU, CYP17A1, MXI1, HRAS, IGF2, RRM1, BRCA2, TP53, ERBB2, ERCC2, and POLD1. Conclusions: MIPs represent a novel technology for highly sensitive and specific gene copy analysis of childhood leukemia. Unique and distinguishing signatures of allelic imbalance can be determined between ALL and AML clinical samples using MIP technology. The unexpected overlap of deleted genes in both ALL and AML may represent a common molecular mechanism that requires further investigation. We currently are adapting MIPs for an expanded cancer probe set and are exploring new techniques to determine loss of heterozygosity (LOH) in pediatric leukemia.
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Reurink, Janine, Adrian Dockery, Dominika Oziębło, G. Jane Farrar, Monika Ołdak, Jacoline B. ten Brink, Arthur A. Bergen, et al. "Molecular Inversion Probe-Based Sequencing of USH2A Exons and Splice Sites as a Cost-Effective Screening Tool in USH2 and arRP Cases." International Journal of Molecular Sciences 22, no. 12 (June 15, 2021): 6419. http://dx.doi.org/10.3390/ijms22126419.

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A substantial proportion of subjects with autosomal recessive retinitis pigmentosa (arRP) or Usher syndrome type II (USH2) lacks a genetic diagnosis due to incomplete USH2A screening in the early days of genetic testing. These cases lack eligibility for optimal genetic counseling and future therapy. USH2A defects are the most frequent cause of USH2 and are also causative in individuals with arRP. Therefore, USH2A is an important target for genetic screening. The aim of this study was to assess unscreened or incompletely screened and unexplained USH2 and arRP cases for (likely) pathogenic USH2A variants. Molecular inversion probe (MIP)-based sequencing was performed for the USH2A exons and their flanking regions, as well as published deep-intronic variants. This was done to identify single nucleotide variants (SNVs) and copy number variants (CNVs) in 29 unscreened or partially pre-screened USH2 and 11 partially pre-screened arRP subjects. In 29 out of these 40 cases, two (likely) pathogenic variants were successfully identified. Four of the identified SNVs and one CNV were novel. One previously identified synonymous variant was demonstrated to affect pre-mRNA splicing. In conclusion, genetic diagnoses were obtained for a majority of cases, which confirms that MIP-based sequencing is an effective screening tool for USH2A. Seven unexplained cases were selected for future analysis with whole genome sequencing.
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Alexiev, Borislav A., and Ying S. Zou. "Clear cell papillary renal cell carcinoma: A chromosomal microarray analysis of two cases using a novel Molecular Inversion Probe (MIP) technology." Pathology - Research and Practice 210, no. 12 (December 2014): 1049–53. http://dx.doi.org/10.1016/j.prp.2014.10.001.

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Pietsch, Torsten, Christian Vokuhl, Gerrit H. Gielen, Andre O. von Bueren, Everlyn Dörner, Glen Kristiansen, Andreas Waha, and Christof Kramm. "HGG-34. DETECTION OF ONCOGENIC FUSION EVENTS IN SUPRATENTORIAL GLIOBLASTOMAS OF YOUNG CHILDREN." Neuro-Oncology 22, Supplement_3 (December 1, 2020): iii349—iii350. http://dx.doi.org/10.1093/neuonc/noaa222.315.

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Abstract INTRODUCTION Glioblastoma in infancy and early childhood is characterized by a more favorable outcome compared to older children, a stable genome, and the occurrence of tyrosine kinase gene fusions that may represent therapeutic targets. METHODS 50 glioblastomas (GBM) with supratentorial location occurring in children younger than four years were retrieved from the archives of the Brain Tumor Reference Center, Institute of Neuropathology, University of Bonn. DNA and RNA were extracted from FFPE tumor samples. Gene fusions were identified by FISH using break-apart probes for ALK, NTRK1, -2, -3, ROS1 and MET, Molecular Inversion Probe (MIP) methodology, and targeted RNA sequencing. RESULTS 37 supratentorial GBM occurred in the first year of life, 13 GBM between one and four years. 18 cases showed fusions of ALK to different fusion partners; all occurred in the first year of life (18/37 cases, 48.6%). Fusions of ROS1 were found in 5, MET in 3, NTRK1, -2, -3 in 10 cases. 12 cases showed no and two novel fusions. The different methods led to comparable results; targeted RNA sequencing was not successful in a fraction of cases. Break-apart FISH led to reliable results on the next day, MIP technology represented the most sensitive method for analysis of FFPE samples. CONCLUSIONS Gene fusions involving the tyrosine kinase genes ALK, MET, ROS1 and NTRK1, -2, -3 occurred in 72% of glioblastomas of children younger than four years; the most frequent were ALK fusions occurring in infant GBM. DNA based MIP technology represented the most robust and sensitive assay.
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Bambury, Richard M., Markus Riester, Joaquim Bellmunt, Edward C. Stack, Lillian Werner, Rachel Park, Gopa Iyer, et al. "Genomic characterization of metastatic urothelial carcinoma." Journal of Clinical Oncology 31, no. 6_suppl (February 20, 2013): 247. http://dx.doi.org/10.1200/jco.2013.31.6_suppl.247.

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247 Background: The genetic profile of primary urothelial carcinoma (UC) has been well documented but no reports analyze specific chromosomal alterations in metastatic disease. We performed molecular inversion probe array (MIP) analysis to compare chromosomal gains or losses in metastatic and primary UC samples. Methods: 33 samples of metastatic UC and 30 primary samples were analyzed from 48 patients (pts), of which paired primary and metastatic tissue was available for 14 pts. DNA from all samples was subjected to molecular inversion probe array analysis to identify focal areas of copy number gain (CNG) or loss (CNL). We focused this analysis on 21 genes from signaling pathways known to be of interest in UC (Table). CNG or CNL was defined as a log2 copy number ratio ≥ 0.8 or ≤ -0.8. GISTIC 2.0 was used to identify significantly altered regions. Results: In the loci analyzed, there were significantly more alterations in metastases than primary samples (8.4% vs 4.3% p=0.002). In particular, there was a significantly higher frequency of E2F3CNG in metastases (27% vs 7% p=0.046). There was frequent discordance in alterations when comparing primary and metastatic tissue from the same patients: 7 of 14 pts harbored potentially oncogenic CNG/CNL in their metastases that were not present in the primary. Conclusions: More alterations in UC-relevant genes were identified in metastases compared with primary tumors, in keeping with the multistep model of cumulative genetic change in cancer progression. More frequent CNG of the E2F3 gene was noted and may represent a mechanism of UC progression. Frequent discordance in alterations between primaries and metastases may be of significant clinical relevance in the future when selecting patients for appropriate molecularly targeted therapy. [Table: see text]
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Dissertations / Theses on the topic "Molecular inversion probe (MIP)"

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Wang, Yuker, Victoria Carlton, George Karlin-Neumann, Ronald Sapolsky, Li Zhang, Martin Moorhead, Zhigang Wang, et al. "High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays." BioMed Central, 2009. http://hdl.handle.net/10150/610039.

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BACKGROUND:A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue.RESULTS:Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE.CONCLUSION:MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
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Akhras, Michael S. "Nucleic Acid Based Pathogen Diagnostics." Doctoral thesis, KTH, Skolan för bioteknologi (BIO), 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4684.

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Pathogenic organisms are transmitted to the host organism through all possible connected pathways, and cause a myriad of diseases states. Commonly occurring curable infectious diseases still impose the greatest health impacts on a worldwide perspective. The Bill & Melinda Gates Foundation partnered with RAND Corporation to form the Global Health Diagnostics Forum, with the goal of establishing and interpreting mathematical models for what effects a newly introduced point-of-care pathogen diagnostic would have in developing countries. The results were astonishing, with potentially millions of lives to be saved on an annual basis. Golden standard for diagnostics of pathogenic bacteria has long been cultureable medias. Environmental biologists have estimated that less than 1% of all bacteria are cultureable. Genomic-based approaches offer the potential to identify all microbes from all the biological kingdoms. Nucleic acid based pathogen diagnostics has evolved significantly over the past decades. Novel technologies offer increased potential in sensitivity, specificity, decreased costs and parallel sample management. However, most methods are confined to core laboratory facilities. To construct an ultimate nucleic acid based diagnostic for use in areas of need, potential frontline techniques need to be identified and combined. The research focus of this doctoral thesis work has been to develop and apply nucleic acid based methods for pathogen diagnostics. Methods and assays were applied to the two distinct systems i) screening for antibiotic resistance mutations in the bacterial pathogen Neisseria gonorrhoeae, and ii) genotype determination of the cancer causative Human Papillomavirus (HPV). The first part of the study included development of rapid, direct and multiplex Pyrosequencing nucleic acid screenings. With improved methodology in the sample preparation process, we could detect an existence of multiple co-infecting HPV genotypes at greater sensitivities than previously described, when using the same type of methodology. The second part of the study focused on multiplex nucleic acid amplification strategies using Molecular Inversion Probes with end-step Pyrosequencing screening. The PathogenMip assay presents a complete detection schematic for virtually any known pathogenic organism. We also introduce the novel Connector Inversion Probe, a padlock probe capable of complete gap-fill reactions for multiplex nucleic acid amplifications.
Patogena organismer smittas till värd organismen genom alla möjliga kontaktnätverk och skapar en mångfald olika sjukdomstillstånd. Dock är det fortfarande vanligt förekommande behandlingsbara infektiösa sjukdomar som orsakar den största hälsoförlusten, sett från ett globalt perspektiv. Bill och Melinda Gates Stiftelsen samarbetade med RAND kooperation för att forma “The Global Health Diagnostics Forum”. Deras mål var att etablera och analysera matematiska modeller för vilka effekter en ny diagnostisk metod utrustat för fältarbete skulle ha i utvecklingsländer. Resultaten var häpnadsveckande, med potentiellt miljoner av liv som skulle kunna räddas på en årlig basis. Den etablerade standarden för diagnostik av patogena bakterier har länge varit kultiveringsmedia baserad. Miljö specialiserade biologer har estimerat att mindre än 1 % av alla bakterie arter går att kultivera. Dock erbjuder genetiska analyser potentialen att kunna identifiera alla mikrober från alla de biologiska rikena. Nukleinsyrebaserade diagnostiska metoder har märkbart förbättrats över de senaste årtionden. Nya tekniker erbjuder utökad sensitivitet, selektivitet, sänkta kostnader och parallella analyser av patient prover. Dock är de flesta metoderna begränsade till standardiserade laboratoriemiljöer. För att konstruera en väl fungerande diagnostisk fältutrustning för användning i problem områden, behöver världsledande tekniker identifieras och kombineras. Fokuseringsområdet för denna doktorsavhandling har varit att utveckla och utföra nukleinsyrebaserade metoder för patogen diagnostik. Metoder och experimentella utförande applicerades på två distinkta system i) sökning av antibiotika resistens relaterade mutationer i den patogena bakterien Neisseria gonorrhoeae och ii) genotypning av det cancer orsakande Humana Papillomaviruset (HPV). Den första delen av studien inriktade sig mot utveckling av snabba, direkta och multiplexa Pyrosekvenserings baserade nukleinsyreanalyser. Med förbättrad provprepareringsmetodologi kunde vi detektera multipla HPV infektioner med högre sensitivitet än vad tidigare beskrivits med liknande metodologi. Den andra delen av studien fokuserades på multiplexa nukleinsyre amplifikationer med “Molecular Inversion Probe” tekniken med sista steg Pyrosekvenserings analys. “PathogenMip assay” erbjuder ett komplett detektionsprotokoll för alla kända patogena organismer. Vi introducerar även den nya “Connector Inversion Probe”, en “Padlock Probe” kapabel att genomföra kompletta gap fyllningar för multiplex nukleinsyre amplifiering.
QC 20100624
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Nordesjö, Olle, Victor Pontén, Stephanie Herman, Joel Ås, Sabri Jamal, and Alona Nyberg. "Ett sannolikhetsbaserat kvalitetsmått förbättrar klassificeringen av oförväntade sekvenser i in situ sekvensering." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-225999.

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In situ sekvensering är en metod som kan användas för att lokalisera differentiellt uttryck av mRNA direkt i vävnadssnitt, vilket kan ge viktiga ledtrådar om många sjukdomstillstånd. Idag förloras många av sekvenserna från in situ sekvensering på grund av det kvalitetsmått man använder för att säkerställa att sekvenser är korrekta. Det finns troligtvis möjlighet att förbättra prestandan av den nuvarande base calling-metoden eftersom att metoden är i ett tidigt utvecklingsskede. Vi har genomfört explorativ dataanalys för att undersöka förekomst av systematiska fel och korrigerat för dessa med hjälp av statistiska metoder. Vi har framförallt undersökt tre metoder för att korrigera för systematiska fel: I) Korrektion av överblödning som sker på grund avöverlappande emissionsspektra mellan fluorescenta prober. II) En sannolikhetsbaserad tolkningav intensitetsdata som resulterar i ett nytt kvalitetsmått och en alternativ klassificerare baseradpå övervakad inlärning. III) En utredning om förekomst av cykelberoende effekter, exempelvisofullständig dehybridisering av fluorescenta prober. Vi föreslår att man gör följande saker: Implementerar och utvärderar det sannolikhetsbaserade kvalitetsmåttet Utvecklar och implementerar den föreslagna klassificeraren Genomför ytterligare experiment för att påvisa eller bestrida förekomst av ofullständigdehybridisering
In situ sequencing is a method that can be used to localize differential expression of mRNA directly in tissue sections, something that can give valuable insights to many statest of disease. Today, many of the registered sequences from in situ sequencing are lost due to a conservative quality measure used to filter out incorrect sequencing reads. There is room for improvement in the performance of the current method for base calling since the technology is in an early stage of development. We have performed exploratory data analysis to investigate occurrence of systematic errors, and corrected for these by using various statistical methods. The primary methods that have been investigated are the following: I) Correction of emission spectra overlap resulting in spillover between channels. II) A probability-based interpretation of intensity data, resulting in a novel quality measure and an alternative classifier based on supervised learning. III) Analysis of occurrence of cycle dependent effects, e.g. incomplete dehybridization of fluorescent probes. We suggest the following: Implementation and evaluation of the probability-based quality measure Development and implementation of the proposed classifier Additional experiments to investigate the possible occurrence of incomplete dehybridization
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Book chapters on the topic "Molecular inversion probe (MIP)"

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Absalan, Farnaz, and Mostafa Ronaghi. "Molecular Inversion Probe Assay." In Comparative Genomics, 315–30. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-515-2_20.

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Ji, Hanlee, and Katrina Welch. "Molecular Inversion Probe Assay for Allelic Quantitation." In Microarray Analysis of the Physical Genome, 67–87. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-192-9_6.

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Conference papers on the topic "Molecular inversion probe (MIP)"

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Jefferson, Keynttisha, Heather Halvensleben, Dawn Green, Ryan Bannen, Michael Brockman, Todd Richmond, and Daniel Burgess. "Abstract 5223: A novel molecular inversion probe (MIP) system for the streamlined identification of germline and somatic sequence variants in cancer." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-5223.

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Wang, Yuker, Ron Sapolsky, Jen Wilkins, Victoria Carlton, Farooq Siddiqui, and Tom Asbury. "Abstract B14: A high-throughput allelic copy-number platform utilizing a 75-ng DNA input in a 330,000 molecular inversion probes (MIP) assay on microarrays with FFPE samples." In Abstracts: AACR International Conference on Translational Cancer Medicine-- Jul 11-14, 2010; San Francisco, CA. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1078-0432.tcmusa10-b14.

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Wang, Yuker, Ron Sapolsky, Sumathi Venkatapathy, Farooq Siddiqui, and Fan Shen. "Abstract 4868: A high-throughput allelic copy-number and somatic mutation platform utilizing a 75-ng DNA input in a 330,000 Molecular Inversion Probes (MIP) assay with FFPE samples." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4868.

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Bannen, Ryan, Michael Brockman, Mark D’Ascenzo, Keynttisha Jefferson, Dawn Green, Heather Halvensleben, Kurt Heilman, Todd Richmond, and Daniel Burgess. "Abstract 5217: Cancer target enrichment panels using advanced molecular inversion probes (MIPs) with ability to reduce amplification bias and detect low frequency variants." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-5217.

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Horn, Candice L., Fabio Nunes, John Calley, Steven Bray, Isabella Wulur, Mark Farmen, Robert Gallavan, et al. "Abstract LB-048: Copy number and loss of heterozygosity (LOH) analysis in 52 breast cancer FFPE samples using molecular Inversion probe array: detailed analysis of reproducibility and performance compared to NGS platforms." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-lb-048.

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Sapolsky, Ron, Anju Shukla, Sumathi Venkatapathy, Chuan Chen, Carsten Bruckner, Vicky Huynh, Liansen Liu, et al. "Abstract 4655: Molecular Inversion Probe analysis using OncoScan™ FFPE Assay Kit to detect copy number aberrations and somatic mutations in lung tumor DNA samples from formalin-fixed paraffin-embedded (FFPE) tissue." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-4655.

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