A SUITE OF WEB TOOLS FOR MORPHOMETRIC, GENETIC, AND MICROARRAY ANALYSIS OF THE MOUSE CNS

1. A SUITE OF WEB TOOLS FOR MORPHOMETRIC, GENETIC, AND MICROARRAY ANALYSIS OF THE MOUSE CNS Glenn Rosen, Melburn Park, Robert Williams, Jonathan Nissanov, and Ken Manly

2. Informatics Center for Mouse Neurogenetics • The Mouse Brain Library - Rosen • iScope -Williams, Park • Neurocartographer - Nissanov • Neurogenetics Tool Box - Manly

3. Goal of Project • Provide online resource for complete mapping of differences in brain structure to defined sets of genes (quantitative train loci; QTLs) • Large scale (e.g., brain weight, volume) • Small scale (e.g., neuron number)

4. Specfic Implementation • Universal Access to Neuroanatomic Phenotypes • Digital Dissection • Comprehensive Genotype Data and Tools for Complex Trait Analysis

5. Universal Access to Neuroanatomic Phenotypes • The Mouse Brain Library • Digital images (0.1–25 µm/pixel) from inbred, RI, and advanced intercross mice. • Ideal for stereologic analysis. • iScope • High-power, through-focus movies. • Microscope controlled over the internet. • Ability to perform neuronal counts on selected regions of selected sections.

6. Digital Dissection • Neurocartographer • Generate 3D atlas of mouse brain. • Use 3D atlas to automatically segment regions of brain.

7. Comprehensive Genotype Data • Databases • RI genotypes and phenotypes • Advanced intercross progeny (G10) • Microarray data from inbred and RI strains • Neurogenetic Tool Box • QTLs without tissue or DNA (WebQTL) • Statistically evaluate neuroanatomic and microarray data with these DBs

8. The Mouse Brain Library

9. Gene Discovery by QTL Mapping • Quantitative Trait Loci • Many medically interesting traits are complex traits • Complex = multiple genes and non-genetic factors • Genes which control complex traits are QTLs • QTLs are detected by statistical associations • Trait values  marker locus genotypes (or estimated genotypes between markers) • Potential QTL indicated by LOD score maximum • Significance measured by LOD score value

10. Evaluate association for many markers and locations between markers significance map location QTL Mapping Principles Marker genotype Trait 1218131017111920... ABAABABB... Progeny individuals

11. QTL Mapping Goals • Significance • Which LOD score maxima correspond to statistically significant QTLs? • Location • How precisely does the LOD score maximum define the QTL location? • Architecture • How many QTLs and what interactions determine a particular trait?

12. LRS statistics from 1000 regressions with permuted data P = 0.05 Permutation Test for Significance Marker genotype Trait 1218131017111920... ABAABABB...

13. .. 200 repetitions. Bootstrap for Location Marker genotype Trait 1218131017111920... ABAABABB...

14. Lateral Ventricles

15. e l c i r t n e V t n e c r e P 4 8 7 4 8 6 7 5 5 6 4 3 0 2 2 2 1 3 1 4 5 0 2 6 1 4 J J 1 1 1 1 1 2 1 1 1 1 2 2 1 2 2 / B A A A B B B A A B B 6 A / A B A A B B B A A A A A B A B X X X X X X X X X X X L X X X X X X X X X X X X X X X A B B B A A A B B A A B B A B B A A A B B B B B A B A 7 5 C Distribution of Ventricle Size 4 3 2 1 0 Strain

16. 20 15 10 5 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Mapping Ventricle Size LRS Score Chromosome

17. Epistatic Interactions

18. The iScope

19. Two Goals for the Online Microscope • Web publication of hard slide libraries • MBL • Pathfinding for other collections • Automatic production of soft libraries

20. Java Interface • Navigation controls • High and low power index views • Quicktime screen

21. Control Pane

22. Navigation Panes • Blue crosshairs show current location • Moveable red dot selects desired location

23. Scheduling

24. Co-development: Focussing Problem • Automatic focussing via proprietary noise-analysis algorithm • Interaction with vendor to obtain custom chip giving us software access to noise value • Focussing can be taken on- of off-board

25. Robotic Slide Library • Commercial design • Smartmotor™ technology • Pneumatic actuators • Changeable cassettes • 6x82 2x3 inch slides

27. Neurocartographer

28. The Navigation Problem

29. T T T T T

30. Atlas (C57BL/6J Male)

31. Atlas Availability • www.neuroterrain.org • www.nervenet.org

32. Blockface Images Section Images Section Images Alignment Parameters Error Detection 2D-2D Rigid- body Alignment Acceptable? Resample Y N Median Filter Reinitiali- zation Reconstruction AIR AIR

33. MacroVoxel Architecture

34. Server-Client MacOStat

35. 2.5D 3D Ordered Unaligned 2D Manual Auto Z-Axis matching 3D Reconstruction Matching Plane Pairs Manual Auto XY Plane matching Matching 3D Features Matching Inplane Features Aligned Sections Warping

36. Parcellation

37. Case 1: test Warping reference Case 2: test

38. Results Case 1 Case 2

39. Next Step

40. Neurogenetics Tool Box (WebQTL)

41. WebQTL

42. WebQTL Mapping Service • http://webqtl.roswellpark.org/ • Mapping populations • Recombinant inbred lines • BxD advanced intercross • No genotyping necessary

43. WebQTL Data Entry • Choice of data entry methods • Choose a data file • Paste or type data

44. WebQTL Data Confirmation • Data entry or confirmation form

45. Mapping Procedures

46. Interval Mapping

47. Interval Mapping Detail

48. Future Directions • MBL • Extend MBL • Improve DB integration • Interface enhancement • On-line image analysis tools • iScope • Additional design and construction • Robotic slide handling • Web archive of through-focus image stacks • Streaming Video • Neurocartographer • Strengthen and extend segmentation algorithm • Segment MBL • Neurogenetics Tool Box • Batch submission of multiple traits • Search for interacting QTLs • Data archiving and export • Additional crosses and cross designs • DNA Array

49. Acknowledgments • This project is part of the Human Brain Project/Neuroinformatics program funded jointly by the National Institute of Mental Health, National Institute on Drug Abuse, and the National Science Foundation (P20-MH 62009).