The document discusses a genome sequence analysis system developed by Hypertable in collaboration with various institutions, aimed at processing biological samples to identify and decode DNA sequences. It highlights the importance of NoSQL for handling large genomic datasets, outlines methodologies for sequencing and alignment, and mentions the use of specific algorithms to discover novel viruses and their taxonomic classifications. Additionally, it describes future enhancements for improving sample analysis through depletion arrays.

1. A Genome Sequence
q
Analysis System Built with
Hypertable
H t bl
Doug Judd
CEO, Hypertable, Inc.

2. Application
Development Team
UCSF-
UCSF-Abbott Viral Diagnostics and
Discovery Center
Director: Dr. Charles Chiu, M.D./Ph.D.
,
http://vddc.ucsf.edu/
Helices Inc.
Taylor Sittler, M.D.
John Dennis
Brad Miller, M.D.
http://helic.es/

3. What is Hypertable?
Modeled after Google’s Bigtable
Google s
Open Source (GPL v2)
Horizontally Scalable
High Performance Implementation (C++)
Thrift Interface for all popular languages
(Java, PHP Ruby Python Perl etc )
(Java PHP, Ruby, Python, Perl, etc.)
NoSQL
No joins (not yet)
No t
N transactions ( t yet)
ti (not t)
Project Started in March 2007

4. Hypertable Deployments

5. Why NoSQL?

6. QuickTime™ d
Q i kTi ™ and a
BMP decompressor
are needed to see this picture.
Source: Nature 458, 719-724 (2009)

7. Source: wired.com, February 2011

8. Genomics 101

9. Base Pair
(aka “base”)
Two nucleotides on opposite
pp
compl. DNA or RNA strands
connected via hydrogen bonds
Double
D bl stranded DNA/RNA i
d d is
made up of base pairs
adenine (A) pairs with thymine (T)
guanine (G) pairs with cytosine (C)
Base-
Base-paired DNA sequence:
ATCGATTGAGCTCTAGCG
TAGCTAACTCGAGATCGC

10. Gene
Encodes info on how to make a protein
DNA or RNA sequence
Thousands t millions of b
Th d to illi f base pairs l
i long
Corresponds to various different biological
traits
Human genome contains about 23,000
g ,
genes

11. Biological Samples
Specimen taken from human or animal
p
Nasal Swabs
Blood Serum
Diarrheal
Cerebral spinal fluid
Sent to a sequencing company to process into
DNA sequence information in digital format
Each sample will g
p generate anywhere from 1M to
y
100M “reads”
A read is a short DNA sequence snippets of
approximately 100 b
i t l bases

12. Example Reads File
GTGGATAGGGGGAGACTAATGTAGTATGATTATCATCATCAACAGAAGCTATGACACCAGGATAAA
CATTTCTTATTGCTGAAAGTATTCTATTGTAGAGATGTACCACAATTTGGTTTCTGGTTTTGTATT
GGGAGGATACTAGGGATTACTGAAGCCAACTTTGCAGACTCATACATTTGACTAGACACAGCC
ACATTACAGTTTTCTGAGGAAAATTCTTAAGATGTTACCCCAAAACATAGCATTTTAAATTAAAAC
GGACCGGCTGAAGCCATGGCAGAAGAACATAAATTGTGAAGATTTCATGGGCATTTATTAGTT
GGAAGTGATAAGTGTCCATGAAATCTTCACAATTTATGTTCAGAGATTGCAGTAAAGACAGGTGTA
AAGACACAGCAAAGCTAAGAGGACCCAACACACGGTAGGGTCGGGGACCTTGGAGAAACATGG
TGGCTTCTTCCTACATGCTTGTGATAGATGACCAAAAAACATTTGTTGAGTTGATGAATAGTACAA
AAAAGGGGCGGATAATAAATGAAAAGGGAATGTGCTGTTATTTCCTACTAAGATCAGAAAGAG
ATATAAACAAAAGCTGTCATCACTTAGGGACTTCAGCCACATAAAACAATGTCAGGCTAGTCACTT
AGAGCTTTGGGACTAGTTGAGTGGCAGCTTAACAAAGCAACGCAATATCCATAGGGATTGGGG
ATATTTACATCTAGTGGATTCTACCAGTATGGTGGTCTTATGTGGACTGCACGTGGTTTTCTAGTA
AGATAGCAGCTCTTCCCAAATTTATTTATAATTGTGGCATTATTTATAATATCAAAATATTAT
GTTGCCAAAGGAGATTAACATTTGAGTCAGTGGGCGGGGTAAGGCCGACCTACCCTTAATCTGGTG
GAGAAAGAAGCTGCTAATGGAGTTTAAAAGGTTACTGTCATTAATGAAAAATAAATTTACAGC
CAGACATTTATGAACAGAAATGGGAAAAACACACTAGGAAAGCACTGCAAAGACTAATCTGTCTTT
AAAGGAGATAGAGTGACTCCAGGCCCCTTAGAAATGACTATACCTGGCAGAGCATGCCAACTG
ATGGGCTCGAGTCCTCACAAATATGAATTCCCCCTAAGTCTTGAGAGGTCATTTGTGCATTTGGAA
GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGTCATACTGCCCA
GCGGGGTTTTTTTTTGTTTCATATTAACTTTAAAGTAGTTTTTTTCCATTTTGTGAAGAAAGACAT
AAAGAACCAAGGCTAATAGTTGTTTGAGTTGTACTTACCATGTTGTTAAATGTCACCTCACAC
CGCTGCCAGCCTATCAGAGCCGGGAATTACACCGTGCTTGGAGTTCTGGCACAGATCCACAGCTAC
AGTTCTTCATTGTAAGAAATGGATGCTAACATGTAACAAGAAAACATCTGAAGGTTAAACTCA
AATAAATGGGTTAATAGTTTGTCTTTCGGTCTTCATACTTTCAATATAAGTGGTTTACTTAGCCGA

13. Sequence Alignment
Arranging the sequences of DNA or RNA to identify
g g q y
regions of similarity
Fuzzy matching algorithm
Alignment methods
Alignment methods
BLAST ‐
BLAST ‐ Basic Local Alignment Search Tool
MegaBLAST
Faster but less accurate alignment methods
Faster but less accurate alignment methods
SOAP ‐
SOAP ‐ Short Oligonucleotide Analysis Package
BLAT ‐ BLAST‐
BLAT ‐ BLAST‐like Alignment Tool

14. Taxonomy
Hierarchical biological classification
Method to group and categorize organisms by
biological type
g yp
Basic Ranks
Kingdom, Phylum/Division, Class, Order, Family, Genus, Species
Downloadable from National Center for
Biotechnology Information (NCBI) website
Every node in the taxonomy tree is assigned a
unique numeric ID

15. GenBank
NIH genetic sequence database
g q
380,000 distinct organisms
126,551,501,141 nucleotide bases
135,440,924 sequence records
Most important and most influential database for
research in almost all biological fields
Growth rate is exponential
Information on each sequence includes:
Numeric ID
Taxonomic information

16. Schema Design

17. Taxa Table
Schema
CREATE TABLE T
Taxa (ID T
(ID, Type, Child
Children, N
Name);
)
Contents
/1 ID 1
/1 ID:fullName /root
/1 Type no rank
/1 Children 1,10239,12884,12908,28384,131567
/1 Name root
/1/10239 ID 10239
/1/10239 ID:fullName /root/Viruses
/1/10239 Type superkingdom
/1/10239 Children 12333,12429,12877,29258,35237, …
/1/10239 Name Viruses
/1/10239/12333 ID 12333
/1/10239/12333 ID:fullName /root/Viruses/unclassified phages
/1/10239/12333 Type no rank
/1/10239/12333 Children 12340,12347,12366,12371,12374, …
/1/10239/12333 Name unclassified phages

18. Reads Table
Schema
CREATE TABLE Reads (Sequence, Quality, GeneKey, Comments);
Contents
AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Sequence ATCGCACCATTGAACTCCAGTC...
AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Quality eeaeeeede_Ycc]dcacab...
AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Comments:qualityFilter 11071815...
AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Sequence GGCTTACGCCTGTAATCCCAGC...
AbCam1_100_ACAGTG,HWI...56#ACAGTG/1 Quality gfee_cgggegggecggggegc...
AbCam1_100_ACAGTG,HWI...56#ACAGTG/1
AbCam1 100 ACAGTG,HWI...56#ACAGTG/1 GeneKey:gnl|GNOMON|1320663.m 11...
AbCam1_100_ACAGTG,HWI...17#ACAGTG/1 Sequence AGGATACGGAAGGCCCAAGGAG...
AbCam1_100_ACAGTG,HWI...17#ACAGTG/1 Quality cdd`dffffffgffgggegf^e...
AbCam1_100_ACAGTG,HWI...17#ACAGTG/1 GeneKey:chr10 110718151643.1308...
AbCam1_100_ACAGTG,HWI...80#ACAGTG/1 Sequence ACGGAAGAGCACACGTCTGAAC...
AbCam1_100_ACAGTG,HWI...80#ACAGTG/1
b 1 100 80# /1 Quality
Q li cbccb[^WUb]_b`_[bR_]...
b b[^ b] b` [b ]
AbCam1_100_ACAGTG,HWI...80#ACAGTG/1 Comments:qualityFilter 11071815...
AbCam1_100_ACAGTG,HWI...88#ACAGTG/1 Sequence GAACTCCAGTCACACAGTGATC...
AbCam1_100_ACAGTG,HWI...88#ACAGTG/1 Quality eeeeeeeeeeeceeeeeaeeTQ...
AbCam1_100_ACAGTG,HWI...88#ACAGTG/1
, Comments:qualityFilter 11071815...
q y

19. Genes Table
Schema
CREATE TABLE Genes (Sequence, TaxID, ID, ReadID);
Contents
1000075 Sequence GAATTCCATGGCAGTAAAACATCTTCCCTTC…
1000075 TaxID 9606
1000075 ID:name HSLFBPS6 Human fructose-1,6-biphosphatase
1000075 ReadID:0310.Lane8big,HWI-EAS355:8:91:1231:1315#0/1 …
1000075 ReadID:0908.Mexus2.TATTAT,SCS:1:22:395:324#0/1_TA …
1000075 ReadID:0916.Enceph2,SCS:6:24:1519:513#0/1
1000075 ReadID:0916.Mexus,SCS:1:22:410:248#0/1
1000075 ReadID:0916.MonkeyAdeno,SCS:2:17:811:769#0/1
1000075 ReadID:0916.MonkeyAdeno,SCS:2:21:1132:1067#0/1
1000075 ReadID:0916.MonkeyAdeno,SCS:2:24:1207:492#0/1
1000075 ReadID:0916.MonkeyAdeno,SCS:2:33:1138:547#0/1
1000075 ReadID:0916.Parecho,SCS:3:4:679:1416#0/1|1
1000075 ReadID:HIV.HIV18_Lane7.s_7_sequence.AAA,SCS:7:30:688 …
1000075 ReadID:HIV.HIV18_Lane7.s_7_sequence.AAA,SCS:7:30:688 …
1000075 ReadID:HIV.HIV18_Lane7.s_7_sequence.unbiased,SCS:7:30 …

20. Monitoring Table Overview

21. Applications

22. Novel Virus Discovery
Process for discovering new viral DNA in a
biological sample
Algorithm Overview
Import biological sample read data from
sequencing company into system
Strip out all reads that align to known DNA
sequences
What’s left over is novel

23. Novel Virus Discovery
Algorithm Detail
Import sample data into Reads table
Run MapReduce program to filter/align reads
and update Comment column of Reads table
p
Filter out poor quality (“low entropy”) reads
Align to common human RNA/DNA
Align to virus database
Align to GenBank
All Reads left in Reads table with no Comment
column are novel

24. Pathogen Discovery
in Cancer Samples
Accomplished using same technique as
novel virus discovery
Matthew Meyerson s Lab @ Broad
Meyerson's
Institute

25. Taxonomic Tree Viewer
Display Taxonomy breakdown of biological
sample
For each aligned read in sample consult
sample,
Genes table to determine Taxonomy ID
Populate HitSummary t bl with t
P l t HitS table ith taxonomy
IDs for all aligned reads from all samples

26. Depletion Array (future)
Align reads to human g
g genome
Determine set of probes - sequences of human
genome with most number of alignments
Send probes to Agilent to produce vial of
“magnetized” DNA sequences of the probes
Mix i l in ith biological
Mi vial i with bi l i l sample l
Magnetized DNA binds to human DNA which
precipitates from solution
Increases viral percentage of sample from
~0.01% - 0.1% to 10 %

27. The End
Questions?