The Kodava Genome Initiative (KGI) is a research project that is initiated and supported by an enthusiastic North-American Kodava community. It has two main goals.

1. To trace the migration pattern and population history of the modern-day Kodavas [ANCESTRY]
   2. To create a reference genetic resource for the Kodava community for future precision medicine efforts [PRECISION MEDICINE].

Starting January 7th 2019, we will start shipping the saliva collection kits to those who are interested in participating in the Kodava Genome Initiative. We are optimistic about collecting 200-300 samples from the North American Kodavas.

Please email me at kodavagenomeinitiative@gmail.com with your names(s) and mailing address for shipping the saliva kits.

We are not funded by any research grants at this time. So, if you wish to donate money to help cover some of the costs, We welcome donations of any amount. No amount is too small.

If you have any questions or suggestions, please feel free to contact Dilip Kodira.

Key individuals leading this project

Dilip Chinnappa Kodira – Dilip is an expert in genomics. He currently serves as the Head of Data Science at PureTechHealth. Dilip led the genome analysis of the first human reference genome at Celera Genomics and Broad Institute of MIT and Harvard. Since then, Dilip has made several key contributions to many high-profile genome sequencing projects. Dilip will be responsible for the overall coordination of this project –including raising funds, planning, sample collection, data analysis and scientific publication.

Naren Ponnappa Anjapravanda – Naren is the Thomas Boat Chair in Cystic Fibrosis Research, Division of Pulmonary Medicine, Research and Director, Cystic Fibrosis Research Center, Division of Pulmonary Medicine, Research at Cincinnati Children’s Hospital. Naren will lead the precision medicine aspect of this project. His research group is involved in developing novel stem cell and genetic editing-based therapeutic options for childhood diseases of the lung and gut.

Maanasa Raghavan – Dr. Raghavan is a molecular anthropologist from the University of Chicago and the lead author of recent paper on “Genomic evidence for the Pleistocene and recent population history of Native Americans”. She will serve as the principal investigator of this project. Maanasa is well-connected with some of the best minds in the molecular anthropology research community and is well-respected for her work on tracing the populations history of worldwide ancestral populations using DNA sequence.

Few FAQ’s on this project

How do you envision accomplishing these goals?

Ancestry:

We will perform Whole Genome Sequencing (WGS) using the latest DNA sequencing technology and employ highly advanced computational methods to analyze this data in conjunction with all the relevant genetic data from many worldwide populations including a few from India.

We will provide the most conclusive scientific evidence via DNA profiling to determine population history of Kodavas and provide clues on our likely migration pattern using genetic similarity to other population groups.

Precision Medicine:

We will use the DNA of a subset of Kodava population in the North America as surrogates for the larger Kodava community in India. We will map the genetic variants to well-known diseases and other phenotypes. We will attempt to discover a few novel variants of wellknown genes. In other words, we hope to generate a reference table containing the types and frequency of well-known common disease-causing variants among the Kodava population. We hope that this resource will spur many future precision medicine efforts in the area of common and rare diseases, and attract further attention and funding from other research agencies.

How is this project funded?

It is a collective initiative of the Kodava community of North America. We are looking for generous donations from the Kodava community. These donations will be used mainly to pay for the cost of sequencing.

Our Principal investigator at University of Chicago will cover expenses for data analysis and interpretation. This will account for more than 65% of the total cost of the project.

We are not funded by any state, federal or non-profit organizations at this time.

Based on the initial feedback, we anticipate participation of nearly 300 subjects which is sufficient for the Ancestry-related analysis.

Why do Whole Genome Sequencing when direct to consumers genetic testing is available for a fraction of the cost?

Whole Genome Sequencing (WGS) is the most comprehensive method as compared to other low-cost smaller hit or miss genetic tests. Those tests target only a limited set of known markers (600,000 markers vs. 3.2 billion letters using WGS) and hence are not suitable for the type of questions we are trying to answer under this project. Also, the markers in these genetic assays are highly biased towards the Caucasian and European populations. If there are any sub-structures present within the Kodava population, we will be able to detect it using our WGS approach. We will be able to generate the first Kodava reference genome using WGS which is impossible to do with limited gene panels.

What is the estimated total cost of this project?

The estimated total cost of this research initiative will be around $126,000.

➢ Total cost will depend on the sample size (no of participants).

For 200 samples, the sequencing cost: $53,800 (@$269 per sample)
Saliva kit, shipping and handling cost: $20-30 per sample
Publication cost -approx. $3000

➢ DNA extraction from saliva ($20 per sample) will be done at University of Chicago (our PI will bear the cost)

➢ Data Analysis: $60,000 (PI, post-doc and a data analyst)- covered fully by our PI at U of Chicago.

How much are you asking from the donors? How will you use these donations?

1. We hope the community is excited and participate in this unique opportunity by donating their saliva samples.
2. We ask the donors to be generous and donate within their capacity. We are not asking for any specific amount.

What if you don’t have enough funds to do the sequencing part?

Hope this never happens. We will go ahead with the original research planning and timing. May pivot a bit and adjust the sample size according the available funds.

What will you do if you have any left-over money after the completion of the project?

If so, any remaining fund will be used to sponsor a young Kodava student to attend a key genomic conference in the continental US.
What is the timeline for this project?

➢ IRB and Research Consent form approval- Dec 15, 2018

➢ Mailing Saliva kit to donors- Jan 15, 2019

➢ Sample collection- Feb 15, 2019

➢ DNA extraction – March15, 2019

➢ Completion of sequencing – April 15, 2019

➢ Data Analysis and Interpretation- Aug 15, 2019

➢ Presentation of the results of the ancestry analysis– Sep1, 2019

➢ Precision Medicine-related data analysis and next steps- Sep 2020

How will you protect the data?

All the data (questionnaire and sequencing) will be deidentified and stored according to the standard research guidelines that protect personal and genomic information. Both Naren and Dilip will not have access to the personal information. Only the PI (Dr. Raghavan) will have access to the questionnaire information provided by the donors. We do not intend to share the collected data with anyone outside the research team.

Can children donate their Saliva samples to this study?

No. We do not have the permission to collect and use samples from anyone under the age group of 21 years.

We may decide to sequence a few trios (father, mother and a child) in the later phase of the project. If and when we do it, we will need to obtain a new IRB that permits the inclusion of children.

What are the benefits of this study to the Kodava community?

Several, none of them are short-term benefits.

1. We hope to provide the first comprehensive DNA-based evidence for tracing the population history and likely migration pattern of Kodavas.
2. Generation of preliminary results will be used for seeking funding from government agencies in the US and elsewhere for future research efforts.
3. A reference genome specific to the Kodava community leading to development of customized diagnostic genetic test panels.
4. Potential opportunities to participate in genomics-based clinical trials with immune therapy, stem-cell and gene-editing modalities of therapeutic options.