重医研究生生物信息考试题目.pdf

1 Bioinformatics examination 1 Final examination schedule 09 12 2014 7 01 2015 four weeks 2 Choose any ONE of the five proposed questions and write a report on design and implementation 3 Report sections a Title page title and personal information including your name student ID major the class number and contact information b Abstract 250 words Keywords 3 5 words c Introduction 2 3 paragraphs d Design and Implementation at least include a flowchart e References please refer to the format of Bioinformatics 4 Requirements a Total words 2000 2500 words not include reference b If you choose the template of Bioinformatics either word or LaTex please disregard the format requirements below c Format requirements Font size Arial 12 宋体 5 号 Line spacing double and Paragraph after 6pt 5 Scores a Fail if the duplication rate 30 in any two of reports two would be considered as plagiarization score 0 Never plagiarize your report b Bonus 10 if written in English please make sure that it is readable and 10 if LaTex used c Bonus 10 if absent one time and 20 if absent two times 6 Please send your report in both the paper and electronic versions NO LATER THAN 7 01 2015 The signed paper should be deposited to the Molecular Genetics Lab at the 3rd floors East building phone number 023 6389 3697 and the compressed electronic file should be sent to Ms Xia Tang at tangxiacqupt 1 Question 1 RNA editing is one of the post or co transcriptional processes with modification of RNA nucleotides from their genome encoded sequence In humans the most prevalent type of RNA editing is mediated by double strand RNA dsRNA specific adenosine deaminase acting on RNA ADAR enzymes which converts adenosines to inosines A to I editing Since I is interpreted as guanosine G during splicing and translation A to I changes in protein coding sequences may lead to codon changes and thus alter functional properties of the proteins RNA editing has been linked to a wide range of human diseases including cancer neurological disorders metabolic diseases viral infection and autoimmune disorder Suppose we aim to study the RNA editome for prostate cancer using next generation sequencing technology Suppose we have collected prostate cancer tissues and the adjacent non cancer tissues from 20 prostate patients please design a pipeline to detect or identify RNA editing sites by comparing RNA seq variants with its counterparts on the genome 2 Question 2 Suppose a family of four members was collected in clinical practice fig 1 including an affected mother an unaffected father an affected offspring daughter founder and an unaffected offspring The affected family contains a series of clinical features and had not been diagnosed with a known disease i e an unidentified syndrome Suppose we aim to study the genetic basis of this family using the technology of whole exome sequencing Please design a study and pipeline to identify the causal mutations that may underline this unidentified syndrome Fig 1 Pedigree 3 Question 3 The APOBEC3B gene is a member of the cytidine deaminase gene family which encodes proteins that are structurally and functionally related to the C to U RNA editing cytidine deaminase APOBEC1 It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control Suppose we aim to perform a bioinformatics analysis on both the mRNA and protein sequence of APOBEC3B Please design a pipeline to download both sequences from online database analyze its promoter regions and transcription factor binding sites and protein domain Furthermore construct an atomic resolution model of APOBEC1 from its amino acid sequence i e the protein 3D structure by homology modeling Note please include your results in the report the Results Section if it was choose 4 Question 4 Electronic medical records EMR are a systematic collection of electronic health information about an individual patient or population which is stored in a digit format Everything related to a patient s care were stored in the EMR including demographic information clinical notes laboratory reports and other accessory tests e g CT and X ray Suppose we aim to construct an EMR database system please state the procedures how to design and implement such a system In addition given the constructed database containing 2 000 patients who have consulted in the Division of Cardiovascular Diseases please design a study to classify these patients with and without coronary heart disease CHD using natural language processing NLP and evaluate your classification procedures 5 Question 5 Gene expression profiling refers to the measurement of the expression of thousands of genes at once which is used to create a global picture of cellular function at the levels of transcriptome The technologies of DNA microarray analog and transcriptome sequencing RNA seq digital have been used to measures the r