Combining Whole-exome and RNA-Seq Data Improves the Quality
... TopHat for WES and RNA-Seq data respectively. Reads that map better to mouse are removed. Human-specific duplicate reads are discarded. After base quality score recalibration, WES Variant detection is performed utilizing GATKLite, Samtools, Freebayes. Samtools only for RNA-Seq data. All variants are ...
... TopHat for WES and RNA-Seq data respectively. Reads that map better to mouse are removed. Human-specific duplicate reads are discarded. After base quality score recalibration, WES Variant detection is performed utilizing GATKLite, Samtools, Freebayes. Samtools only for RNA-Seq data. All variants are ...
Lesson 3 | DNA and Genetics
... 3. Choose four colors of chenille stems. Each color represents one of the four nitrogen bases. Record the color of each nitrogen base in your ...
... 3. Choose four colors of chenille stems. Each color represents one of the four nitrogen bases. Record the color of each nitrogen base in your ...
Regulatory region variability in the human presenilin-2
... We have analyzed the 5⬘-upstream promoter region of the presenilin 2 gene (PSEN2) for regulatory elements and examined Alzheimer disease (AD) patients and non-demented individuals for polymorphisms in the 5⬘ upstream promoter region of the PSEN2 gene. Direct sequencing analysis detected a common sin ...
... We have analyzed the 5⬘-upstream promoter region of the presenilin 2 gene (PSEN2) for regulatory elements and examined Alzheimer disease (AD) patients and non-demented individuals for polymorphisms in the 5⬘ upstream promoter region of the PSEN2 gene. Direct sequencing analysis detected a common sin ...
Using E. coli as a model to study mutation rates
... E−8 per base per generation. This variation is caused, in part, by uncertainty or assumptions in key parameters, such as divergence times between species, generation times and ancestral population sizes. Furthermore, all previous estimates represent an average across multiple generations and/or an a ...
... E−8 per base per generation. This variation is caused, in part, by uncertainty or assumptions in key parameters, such as divergence times between species, generation times and ancestral population sizes. Furthermore, all previous estimates represent an average across multiple generations and/or an a ...
The “silent” noise of bacterial genes…
... Research scientists from INRA, AgroParisTech, CNRS, INSERM and the University of Montpellier have succeeded in observing the expression of bacterial genes with an unprecedented accuracy. Using fluorescence-based techniques and microscopy, the scientists were able to count the number of synthesized p ...
... Research scientists from INRA, AgroParisTech, CNRS, INSERM and the University of Montpellier have succeeded in observing the expression of bacterial genes with an unprecedented accuracy. Using fluorescence-based techniques and microscopy, the scientists were able to count the number of synthesized p ...
The Hunt for Immortality
... be born. Watson thought about this, because the method a chromosome uses to replicate itself during cell division should, logically, destroy some of the genes at the ends of the DNA. Watson called this the end-replication problem. By the mid-1970s, scientists knew the answer to this puzzle. There wa ...
... be born. Watson thought about this, because the method a chromosome uses to replicate itself during cell division should, logically, destroy some of the genes at the ends of the DNA. Watson called this the end-replication problem. By the mid-1970s, scientists knew the answer to this puzzle. There wa ...
Thyroid Nodules
... All patients with MTC should be tested for RET mutations. (point mutations that induce constitutive activity of the tyrosine kinase .) ...
... All patients with MTC should be tested for RET mutations. (point mutations that induce constitutive activity of the tyrosine kinase .) ...
Doug Juvinall December 8, 2009 Bradley University Bio 464 Lab
... TTHERM 00192000 was measured during conjugation of the ciliate Tetrahymena. TTHERM 00192000 was named CYC5. RNA was collected from Tetrahymena at different time points of conjugation. Primers were made for the TTHERM 00192000 gene which was then used for the RTPCR. The intensities of the gel were de ...
... TTHERM 00192000 was measured during conjugation of the ciliate Tetrahymena. TTHERM 00192000 was named CYC5. RNA was collected from Tetrahymena at different time points of conjugation. Primers were made for the TTHERM 00192000 gene which was then used for the RTPCR. The intensities of the gel were de ...
spermatoenesis oogenesis crossing over
... So… even though two copies of a given gene are inherited, one from each parent, only the maternal or paternal allele is expressed. The non-expressed allele is said to be “imprinted.” ...
... So… even though two copies of a given gene are inherited, one from each parent, only the maternal or paternal allele is expressed. The non-expressed allele is said to be “imprinted.” ...
Gene Section PF4 (platelet factor 4) Atlas of Genetics and Cytogenetics
... Platelet content of CXCL4 in 35 patients with colon cancer was shown to be significantly increased when compared to 84 age-matched healthy controls (Peterson et al., 2012). Though not thought to be clinically relevant, a change in CXCL4 platelet levels was identified as a predictor of colorectal car ...
... Platelet content of CXCL4 in 35 patients with colon cancer was shown to be significantly increased when compared to 84 age-matched healthy controls (Peterson et al., 2012). Though not thought to be clinically relevant, a change in CXCL4 platelet levels was identified as a predictor of colorectal car ...
Suracell: My Test Results
... together. If the DNA of any two individuals were compared, a variation would be found approximately once in every two thousand letter positions and this variation is the SNP. These variations are completely normal and occur frequently in the general population. We have taken a sample of your cells f ...
... together. If the DNA of any two individuals were compared, a variation would be found approximately once in every two thousand letter positions and this variation is the SNP. These variations are completely normal and occur frequently in the general population. We have taken a sample of your cells f ...
Gene Section polypeptide 1)
... for heterozygosity of the minor alleles are taken from NCBI. ND: not determined. ...
... for heterozygosity of the minor alleles are taken from NCBI. ND: not determined. ...
Teacher notes and student sheets
... variation in actual number means average not necessarily whole number two unusual CF mutations very rare/ 6 a year therefore average (0.1) less than a whole number in sample of 10 000 3.5 x 60 = 210 actual babies a year (or other similar calculation showing how sample gives non-integer values) ...
... variation in actual number means average not necessarily whole number two unusual CF mutations very rare/ 6 a year therefore average (0.1) less than a whole number in sample of 10 000 3.5 x 60 = 210 actual babies a year (or other similar calculation showing how sample gives non-integer values) ...
Recombinant DNA
... • Gene therapy is the insertion of genetic material into human cells for the treatment of genetic disorders, cardiovascular disease and cancer. • Various methods of gene transfer have been used. – Viruses, genetically modified to be safe, can be used to introduce a normal gene into the body. – Lipos ...
... • Gene therapy is the insertion of genetic material into human cells for the treatment of genetic disorders, cardiovascular disease and cancer. • Various methods of gene transfer have been used. – Viruses, genetically modified to be safe, can be used to introduce a normal gene into the body. – Lipos ...
Chapter 7 Molecular Genetics: From DNA to Proteins
... Hershey and Chase Seal the Deal The conclusion that DNA is the genetic material was not widely accepted at first. It had to be confirmed by other research. In the 1950s, Alfred Hershey and Martha Chase did experiments with viruses and bacteria. Viruses are not cells. They are basically DNA inside a pr ...
... Hershey and Chase Seal the Deal The conclusion that DNA is the genetic material was not widely accepted at first. It had to be confirmed by other research. In the 1950s, Alfred Hershey and Martha Chase did experiments with viruses and bacteria. Viruses are not cells. They are basically DNA inside a pr ...
The Importance of Genetic Testing
... – 1/3 non-carriers • ~15-20% recurrence in future pregnancies • Maternal and paternal origin reported ...
... – 1/3 non-carriers • ~15-20% recurrence in future pregnancies • Maternal and paternal origin reported ...
PATIENT REPORT Patient: Medical Record/Patient #:
... invasion (p = 0.007) were significantly associated with metastasis (Table 2). Kaplan-Meier analysis rendered similar results. When all three significant variables were entered into a Cox multivariate model, only the Class 2 molecular signature exhibited significant association with metastasis. Compa ...
... invasion (p = 0.007) were significantly associated with metastasis (Table 2). Kaplan-Meier analysis rendered similar results. When all three significant variables were entered into a Cox multivariate model, only the Class 2 molecular signature exhibited significant association with metastasis. Compa ...
PCR-technique Applications
... - Binding + reverse transcription complementary DNA-strand produced - DNA synthesis with PCR - a fluorescent dye is added to get probe 2 ...
... - Binding + reverse transcription complementary DNA-strand produced - DNA synthesis with PCR - a fluorescent dye is added to get probe 2 ...
Mcbio 316 – Exam 1 Page 1 (5) 1. Strains with a mutD mutation
... ANSWER: More DNA replication occurs during fast growth than during slow growth conditions. During rapid growth, initiation of DNA replication occurs more often, resulting in an increased number of DNA replication forks. (DNA polymerase does not work any faster, there are just more DNA replication oc ...
... ANSWER: More DNA replication occurs during fast growth than during slow growth conditions. During rapid growth, initiation of DNA replication occurs more often, resulting in an increased number of DNA replication forks. (DNA polymerase does not work any faster, there are just more DNA replication oc ...
Genetics and Nephrotic Syndrome
... could be primary drivers of nephrotic disease protein coding regions 1% of the human genome but harbor 85% of mutations with large effects on diseaserelated traits ...
... could be primary drivers of nephrotic disease protein coding regions 1% of the human genome but harbor 85% of mutations with large effects on diseaserelated traits ...
Essential Genetics for Horsemen
... present, whether a foal has one ‘E’ or two (Ee or EE). The ‘e’ allele produces a chestnut (red) base color, but if an ‘E’ allele is present with an ‘e’ the base coat color is black (Ee). For a chestnut color to be produced, the foal needs to have two copies of the ‘e’ allele (ee). So, a foal that r ...
... present, whether a foal has one ‘E’ or two (Ee or EE). The ‘e’ allele produces a chestnut (red) base color, but if an ‘E’ allele is present with an ‘e’ the base coat color is black (Ee). For a chestnut color to be produced, the foal needs to have two copies of the ‘e’ allele (ee). So, a foal that r ...
Genetics and Epigenetics of Human Disease
... gene is silenced depending on whether it was inherited from father or from mother. The molecular silencing process (DNA methylation) involved in genomic imprinting is a classic example of epigenetic regulation, in which there is an enduring change in gene activity but without any change in DNA seque ...
... gene is silenced depending on whether it was inherited from father or from mother. The molecular silencing process (DNA methylation) involved in genomic imprinting is a classic example of epigenetic regulation, in which there is an enduring change in gene activity but without any change in DNA seque ...
Document
... • As the number of GO terms for which test significance is large, p_values have to take the correction for multiple tests in account. For instance: o Methods controlling False Discovery Rate (FDR): Benjamin and Hochberg (assuming independence) Benjamin and Yekutieli (dropping independence) ...
... • As the number of GO terms for which test significance is large, p_values have to take the correction for multiple tests in account. For instance: o Methods controlling False Discovery Rate (FDR): Benjamin and Hochberg (assuming independence) Benjamin and Yekutieli (dropping independence) ...
Oncogenomics
Oncogenomics is a relatively new sub-field of genomics that applies high throughput technologies to characterize genes associated with cancer. Oncogenomics is synonymous with ""cancer genomics"". Cancer is a genetic disease caused by accumulation of mutations to DNA leading to unrestrained cell proliferation and neoplasm formation. The goal of oncogenomics is to identify new oncogenes or tumor suppressor genes that may provide new insights into cancer diagnosis, predicting clinical outcome of cancers, and new targets for cancer therapies. The success of targeted cancer therapies such as Gleevec, Herceptin, and Avastin raised the hope for oncogenomics to elucidate new targets for cancer treatment.Besides understanding the underlying genetic mechanisms that initiates or drives cancer progression, one of the main goals of oncogenomics is to allow for the development of personalized cancer treatment. Cancer develops due to an accumulation of mutations in DNA. These mutations accumulate randomly, and thus, different DNA mutations and mutation combinations exist between different individuals with the same type of cancer. Thus, identifying and targeting specific mutations which have occurred in an individual patient may lead to increased efficacy of cancer therapy.The completion of the Human Genome Project has greatly facilitated the field of oncogenomics and has increased the abilities of researchers to find cancer causing genes. In addition, the sequencing technologies now available for sequence generation and data analysis have been applied to the study of oncogenomics. With the amount of research conducted on cancer genomes and the accumulation of databases documenting the mutational changes, it has been predicted that the most important cancer-causing mutations, rearrangements, and altered expression levels will be cataloged and well characterized within the next decade.Cancer research may look either on the genomic level at DNA mutations, the epigenetic level at methylation or histone modification changes, the transcription level at altered levels of gene expression, or the protein level at altered levels of protein abundance and function in cancer cells. Oncogenomics focuses on the genomic, epigenomic, and transcript level alterations in cancer.