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Statistical Genetics 統計遺伝学

Statistical Genetics 統計遺伝学. 2012/04/18 Ryo Yamada Unit of Statistical Genetics Center for Genomic Medicine Graduate School of Medicine Kyoto University. Today’s contents. Statistical Genetics Genotype and Phenotype Graph to understand relations Mathematical approach

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Statistical Genetics 統計遺伝学

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  1. Statistical Genetics統計遺伝学 2012/04/18 Ryo Yamada Unit of Statistical Genetics Center for Genomic Medicine Graduate School of Medicine Kyoto University

  2. Today’s contents • Statistical Genetics • Genotype and Phenotype • Graph to understand relations • Mathematical approach • Dynamics and differentiation

  3. 太陽 おけら てのひら みみにみみず あめんぼ みつばち とんぼ 私が両手をひろげても、 　　　お空はちっとも飛べないが、 　　　飛べる小鳥は私のやうに、 　　　地面（じべた）を速くは走れない。 　　　私がからだをゆすっても、 　　　きれいな音は出ないけど、 　　　あの鳴る鈴は私のやうに、 　　　たくさんな唄は知らないよ。 　　　鈴と、小鳥と、それから私、 　　　みんなちがって、みんないい。 かえる

  4. 瓜二つ 瓜の蔓に茄子はならぬ 鳶が鷹を生む カエルの子はカエル

  5. What to study?How to study? What do you want to know? How do you want to know it?

  6. Genetics • Genotype • Phenotype

  7. Genetics • Genotype • Phenotype • Identity • Variation How to grab “Genotype” and “Phenotype” with their “Identity” and “Variation”. One way is to make a catalogue of facts among “them”. The other way is to give a strategy to make the catalogue.

  8. Genotype Phenotype Intermediate phenotype Terminal phenotype

  9. Graph (Theory)グラフ(理論)

  10. Pedigree 家系図

  11. Pedigree 家系図 phylogenetic tree 系統樹

  12. Phylogety, a tree

  13. Distance 距離

  14. Distance: More than one definition 距離にもいろいろな定義がある

  15. Make graph from distance info距離情報からグラフを作る Distance is a way to quantitate relation. Three items that make a triangle can be connected as a star without changing their pathway-distance.

  16. Difference among graphsグラフ間の違い Same or different as a tree?

  17. Difference among graphsグラフ間の違い Topology (Shape) and length of edges 位相(形)と辺の距離 Same or different as a tree?

  18. Items can be expressed as a tree when distance among them are given. Different “distances” give different trees.

  19. Graphs for data-analysesグラフによるデータ解析

  20. Heatmap Data-mining approach also uses trees.

  21. Tree needs “distance” with its definition. Clustering methods also need definition to make tree structure..

  22. Data give trees and change the order in items. When the order in items are not changed and when relation among the items are displayed, it is correlation matrix.

  23. Relations among columns Original data Relations among lines Relations among columns and lines

  24. Pedigrees are NOT graphs家系図はグラフでは　ない

  25. Trees in classical genetics: Pedigrees

  26. Relation between humans. Relation between chromosomes.

  27. A human relation can be multiple chromosomal relations.

  28. Chromosomes have two parental chromosomes. But a base has only one parental base.

  29. Sexual and Asexual ReproductionGraph有性生殖と無性生殖、とグラフ

  30. Genotype Phenotype Intermediate phenotype Terminal phenotype

  31. Types of Dataデータ タイプ

  32. Categorical data and sets. カテゴリ型データと集合

  33. Ordered and Non-ordered.

  34. High-dimensional data and graph

  35. Genotype Phenotype Intermediate phenotype Terminal phenotype

  36. Networksネットワーク

  37. DNA塩基配列バリアント DNA配列 エピゲノム修飾 ? 次世代 シークエンス eQTL ? ネットワーク (転写物・翻訳物) ? ? ? GWAS ? E1 E2 E3 疾患に共通する因子 E4 E5 D1 疾患とその亜分類 D2 D1a D1b D2b D3 D5 D4 D2a D2c

  38. Components of graphs グラフの部品 Concepts of regulations/interactions 制御/相互関係の概念 Graphs are being used for biology

  39. Networks are complexネットワークは複雑

  40. We can not grab the graph as a whole at onceグラフ全体を一発で了解することは無理

  41. Transition of Stata状態推移 step-by-step順番に Markov-chain マルコフ連鎖 Bayesian networks ベイズネットワーク

  42. Genetic Heterogeneity and Transition of Stata遺伝的多様性と状態推移 Three components to make genetic heterogeneity 遺伝的多様性を作る３要素 Mutations Recombinations Genetic drifts 変異 組換え 遺伝的浮動 Variants will drift out from the world.

  43. 疾患原因・薬剤応答性遺伝因子探索GWAS

  44. Complementary strand, for what?

  45. Cross-overs and recombinatios

  46. What is the relation between crossovers and identity of origin?

  47. What is the distribution of segment-length between crossovers? Exponential...

  48. Some chromosomes leave many copies but others none.

  49. Variants will drift out from the world.

  50. Chromosomal relations in generations.

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