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I have been interested in genome analysis since reading that Steve Jobs had his own genome analyzed and looking at the reduced time this now takes.

“SAP HANA Enabling Genome Analysis” was ASUG webcast given last month.  Speakers included Dr. Joanna Kelley of Stanford University and Enakshi Singh of SAP HANA Product Management.   They reviewed the use cases for HANA with genome analysis.

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Figure 1: Source: SAP

The first use case is for the clinician as shown in Figure 1.  Genetic variants may cause umor formation in cancer

The needs is for a genetic profile that is more personalized

Doctor/nurse can look at data on iPad for HANA to enable personalized treatment.

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Figure 2: Source: SAP

Figure 2 shows the use case for the researcher, who wants to see what patterns exist with people in autism.

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Figure 3: Source: SAP

Figure 3 explains genetic variants.  The speaker said that a mistake in genetic data can cause colossal effects.

The entire set of genetic information is called a genome.

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Figure 4: Source: SAP

Figure 4 shows that costs are going down to analyze the Human Genome.  It used to take 13 years to sequence one genome.  In the past, sequencing, processing and computational were a bottleneck

The cost per base is declining steadily.

The green line in figure 4 shows the quality of basis.

Today there are devices that are not on market to allow you to sequence it at your fingertips

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Figure 5: Source: SAP

Figure 5 shows how big the data is 800MB for one genome.  This explains why it is “big data”.

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Figure 6: Source: SAP

Figure 6 shows that SAP HANA was 17 times faster with genome analysis than BWA, which took 84 hours in BWA and it took SAP HANA 5 hours.

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Figure 7: Source: SAP

Figure 7 shows that 1000 Genomes Project, and the speaker said it is now up to 2500 individuals.

Now the genome data is available for researchers, they can analyze queries, get new insights

They have variant data for 629 individuals

They have 12B entries in table for data model, with 293 GB, which gets compressed in SAP HANA with a 4x compression ratio

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Figure 8: Source: SAP

Figure 8 shows they use R, which is used by researchers for stats and query results.

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Figure 9: Source: SAP

Figure 9 is the future, they want to make best decision possible

Researchers to look at 1000s of genomes; analyze results in real-time

Question and Answer:

Q: Rather than in memory and R support what else does HANA do?

A: HANA compresses memory, can write SQL and SQL script

Column store architecture – run queries faster

Q: Who else can use this solution?

A: expand to clinicians, doctors, beyond Stanford

Pharmaceuticals for clinical trials; chemo doesn’t work for certain genetics

Insurance companies interested in genetic data

Related Links:

Mark Heff Blog: HANA and the future of Personal… | SCN

Why Big Data Matters – ASUG Webcast Summary

ASUG BusinessObjects User Conference Keynotes – you can watch this week online at this link  – will Big Data be a topic?

SAP Big Data Website

Diginomica’s Big Data Rant Article


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4 Comments

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    1. Kumar Mayuresh

      Hi Peter,

      MKI is doing great job by Using SAP HANA, but would be great if majority of the pharmaceutical industry uses HANA for their research, ultimately making the world more healthier and happier.

      Regards

      Kumar 🙂

      (0) 

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