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Hadoop as a Platform for Genomics
The document discusses the evolution of DNA sequencing and its implications for genomics, emphasizing the shift from research-focused applications to clinical analytics and personalized medicine. It highlights various analytics applications, including genomic data analysis and forensic applications, while addressing the need for scalable processing solutions beyond traditional Hadoop. Additionally, the document references India's Aadhaar initiative as an example of leveraging biometric data management in large-scale identity verification, drawing parallels to genomic data processing.
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Hadoop as a Platform for Genomics
- 1. Hadoop as aPlatform for Genomics @AllenDay, Chief Scientist Sungwook Yoon, Data Scientist Data Science @MapR
- 2. ® © 2014 MapRTechnologies 2 DNA Sequencing, pre-2004 years CPU transistors/mm2 HDD GB/mm2 DNA bp/$, pre-2004
- 3. ® © 2014 MapRTechnologies 3 DNA Sequencing, 2004 Disruption years CPU transistors/mm2 HDD GB/mm2DNA bp/$, post-2004 DNA bp/$, pre-2004
- 4. ® © 2014 MapRTechnologies 4 DNA Sequencing, 2004 Disruption years CPU transistors/mm2 HDD GB/mm2DNA bp/$, post-2004 DNA bp/$, pre-2004 Similar disruption occurred for Internet traffic in mid-1990s
- 5. ® © 2014 MapRTechnologies 5 Effect: Many DNA-Based Apps Coming… • 2014: US$ 2B, mostly research, mostly chemical costs • 2020: US$ 20B, mostly clinical, mostly analytics costs Macquarie Capital, 2014. Genomics 2.0: It’s just the beginning 0 5 10 15 20 25 2014 2020 Clinical Non-Clinical
- 6. ® © 2014 MapRTechnologies 6© 2014 MapR Technologies ® 1. What Kind of Analytics Apps? 2. How do they Work?
- 7. ® © 2014 MapRTechnologies 7 Target Audience • Fluency in computing, math • Basic knowledge of genetics, DNA …so expect some encapsulated complexity http://xkcd.com/803/
- 8. ® © 2014 MapRTechnologies 8 Clinical Sequencing Business Process Workflow PhysicianPatient Clinic blood/saliva Clinical Lab Analytics extract
- 9. ® © 2014 MapRTechnologies 9 Step 1: Identify all the Single Nucleotide Polymorphisms • Currently ~12MM known SNPs • Each person has a unique Genotype – Typically 3-5MM SNPs – Relative to a reference human – diff this.human other.human, essentially • Inherited from parents • Inexpensive to find as sequencing costs have plummeted http://learn.genetics.utah.edu/content/pharma/snips/
- 10. ® © 2014 MapRTechnologies 10 Step 2: Characterize all the SNPs (ML, AI) Other data & algorithms JOIN
- 11. ® © 2014 MapRTechnologies 11 Innovation Opportunities Pop. Freq Drug A Response Drug B Response 10% Good Good 30% Poor Fair 30% Excellent Poor 30% Good, but Toxic Fair “Nil nocere” – do no harm Step 3: Use Genotype to Customize Therapy
- 12. ® © 2014 MapRTechnologies 12 Jan 30: Obama Unveils “Precision Medicine” Initiative “Most medical treatments have been designed for the ‘average patient’ … treatments can be very successful for some patients but not for others.” http://www.msnbc.com/msnbc/obama-seeks-215-million-personalized-medicine
- 13. ® © 2014 MapRTechnologies 13 Application: Forensic Analysis http://cgi.uconn.edu/stranger-visions-forensic-art-exhibit/ http://snapshot.parabon-nanolabs.com/ http://www.nature.com/news/mugshots-built-from-dna-data-1.14899
- 14. ® © 2014 MapRTechnologies 14 http://steamcommunity.com/app/203160/discussions/0/846956188647169800/ http://www.vox.com/2015/2/1/7955921/lara-croft-moores-law Moore’s Law #Dataviz: Lara Croft 230=>40,000 Polygons (1996-2014)
- 15. ® © 2014 MapRTechnologies 15© 2014 MapR Technologies ® 1. What Kind of Analytics Apps? 2. How do they Work?
- 16. ® © 2014 MapRTechnologies 16 Genome Sequencing in a Nutshell Reference HumanPatient Reference Genome ¢ ¢ ¢ ¢ ¢ ¢ ¢ De novo sequencing + assemblyResequencing Patient Genotype
- 17. ® © 2014 MapRTechnologies 17 Population-Scale Genome Biobanking
- 18. ® © 2014 MapRTechnologies 18 GATK: Typical Tool for DNA=>Genotype Conversion Advantages • No consensus alternative… yet • Works! • Already deployed and being used to save lives Disadvantages • Map-Reduce but not Hadoop (and no plans to support) • Compute context cannot span multiple nodes • Inefficient use of shared memory (even within one node) • Inefficient asymmetric joins. No leverage of context, data locality
- 19. ® © 2014 MapRTechnologies 19 GATK: flat after chromosome split
- 20. ® © 2014 MapRTechnologies 20 Big Picture N DNA Input Records All SNPs Catalog still growing; Genotype space huge ≫ 8E37 Personal input is fixed N records and trivial to cut into P partitions GG A good implementation: scales O(N) ~ F(N,P) But GATK is SLOW: scales O(N) ~ F(Genotypes) GATK parallelization metrics / DEAD END attempts: https://github.com/allenday/sequencing-utils
- 21. ® © 2014 MapRTechnologies 21 Bigger Picture: Human Suffering • Widely disliked. Reduction of suffering is good business. Even Bigger • Is it morally wrong to allow others to suffer? • If you agree, and there’s a way to reduce suffering, then… • We can argue there is a moral imperative to build the most efficient, dependable, inexpensive solution possible
- 22. ® © 2014 MapRTechnologies 22© 2014 MapR Technologies ® From Feasible to Easy & Efficient
- 23. ® © 2014 MapRTechnologies 23 Two Phases of Genome Data Analysis • Batch Sequence Processing – Align the reads to correct location – Make correct Variants detection through statistical modeling • Genome / Phenome Data Analysis – Find relevant Genotypes for Phenotypes – Find relevant Phenotypes for Genotypes
- 24. ® © 2014 MapRTechnologies 24 Genome Processing Requirements Big Storage Big Memory Algorithms Sorting Group By Clustering Sparse Matrix Distributed Processing Which Free SW Has This Solution? 2TB per person Affordable Hardware Forward Backward
- 25. ® © 2014 MapRTechnologies 25 Genome Processing Needs More Than Hadoop • Strong In Memory Computation • Strong Sparse Matrix Computation Which Free SW Has This Solution?
- 26. ® © 2014 MapRTechnologies 26 Still One More Genome Data Format Definition (A 1 Z) (B 1 Z) (C 1 Z) A 1 Z B 1 Z C 1 Z A B C 1 1 1 Z Z Z Record 1 Record 2 Record 3 RowBased ColBased Sorting Group MLLib
- 27. ® © 2014 MapRTechnologies 27 Compute Engines Data Workflow Adam Pipeline FastQ BAM ADAM ADAM- VCF VCF AvocadoADAM ADAMAligner Super Fast • In-memory • Scalable compute context Pipeline in Genomics Data Workflow, a sequence of data transformation from DNA sequence read to Variant Calls
- 28. ® © 2014 MapRTechnologies 28 Scale with Machines From ADAM Tech Report
- 29. ® © 2014 MapRTechnologies 29 That’s A lot but it just is a start • Why do we want sequencing? – To catch criminals ?? • Police State?? • Deeper wider genome study may reveal – Future medicine – Cure for diseases – Maybe … find Heroes??
- 30. ® © 2014 MapRTechnologies 30 Variants Accumulate – Need a Scalable Variant Store ADAM ADAM- VCF
- 31. ® © 2014 MapRTechnologies 31 Genome × Phenome Analysis For given population, given SNP 𝛿, and given phenotype ϕ: Count the number of occurrences as the value of the matrix 𝛿5 ϕ5 ϕ3 ϕ1 𝛿3 𝛿1 SPARSE Billion + Phenotypes SPARSEBillion+Genotypes
- 32. ® © 2014 MapRTechnologies 32 Interpreting Genome × Phenome Matrix Factorization Result • Row Vectors of X represents – Archetype set of phenotypes • Column vectors of Y represents – Archetype set of genotypes 𝛿5 ϕ5 ϕ3 ϕ1 𝛿3 𝛿1 Principal Column Vector Archetype Genotypes Archetype Phenotypes Principal Row Vector Sparse Matrix Package is Actively Developed in Spark Community
- 33. ® © 2014 MapRTechnologies 33 Toward Heroes : Genome × Phenome Tensor • Aggregating over individuals with matrix could ignore the correlations among genotypes and phenotypes • Maintain individual identity Variants Phenotypes Variants Phenotypes
- 34. ® © 2014 MapRTechnologies 34 Tensor Factorization (Parafac) Genome Variants Phenome ≈ Principal Variants1 Principal Phenotypes1
- 35. ® © 2014 MapRTechnologies 35© 2014 MapR Technologies ® From Imaginable to Possible
- 36. ® © 2014 MapRTechnologies 36 Genome needs Hadoop Variant Calling DNA Sequencer Reads Reference Genome Genotype/ Phenotype/ Individual Matrix Cure & Prevent Disease Medical Records Patient
- 37. ® © 2014 MapRTechnologies 37 Scalable Variant Store – Data Mining Model P ~ F(G) Fortunately, this has already been done… Genotypes Med Record Phenotypes, e.g. disease risk, drug response
- 38. ® © 2014 MapRTechnologies 38 Largest Biometric Database in the World PEOPLE 1.2B PEOPLE
- 39. ® © 2014 MapRTechnologies 39 Why Create Aadhaar? • India: 1.2 billion residents – 640,000 villages, ~60% lives under $2/day – ~75% literacy, <3% pay income tax, <20% have bank accounts – ~800 million mobile, ~200-300 million migrant workers • Govt. spends about $25-40 billion on direct subsidies – Residents have no standard identity document – Most programs plagued with ghost and multiple identities causing leakage of 30-40% Standardize identity => Stop leakage
- 40. ® © 2014 MapRTechnologies 40 Aadhaar Biometric Capture & Index Raw Digital Fingerprint
- 41. ® © 2014 MapRTechnologies 41 Aadhaar Biometric ID Creation F(x): unique features G(x): uncommon features H(x): other features • 900MM people loaded in 4 years • In production – 1MM registrations/day – 200+ trillion lookups/day • All built on MapR-DB (HBase)
- 42. ® © 2014 MapRTechnologies 42 How Does this Relate to Genomics? F(x): unique features G(x): uncommon features H(x): other features Same data shape and size • Aadhaar: 1B humans, 5MB minutia • Genome: 7B humans, ~3M variants
- 43. ® © 2014 MapRTechnologies 43 How Does this Relate to Genomics? F-1(x): common features F(x): unique features G(x): uncommon features H(x): other features Same data shape and size • Aadhaar: 1B humans, 5MB minutia • Genome: 6B humans, ~3M variants • Genome: variant × phenotype • Common variant => effect-causing gene F-1(x) ! Same data set operations
- 44. ® © 2014 MapRTechnologies 44 Genotype/ Phenotype/ Individual Matrix ≈ individuals fingerprint minutiae Find genetic basis of fingerprints medicalrecords genetic variants Find genetic basis of disease
- 45. © 2014 MapRTechnologies, confidential ® Thanks! Questions? @allenday, @mapr aday@mapr.com, syoon@mapr.com linkedin.com/in/allenday