Shaping the Future of Precision Medicine for Newborns

A Recap of Frontiers in Pediatric Genomic Medicine Conference

Rady Children’s Institute for Genomic Medicine’s (RCIGM) Frontiers in Pediatric Genomic Medicine Conference took place last week on the scenic shores of La Jolla, California. The third annual conference brought together innovators from children’s hospitals and genetics labs around the world who are making big strides in the field of pediatric genomics.  

The meeting began each day with a poignant patient story. Parents held their infant on stage while sharing the story of the very emotionally-trying start to their baby’s life. In all cases these babies were admitted to Rady’s NICU at less than one week old with unexplainable medical conditions linked to the nervous system. With no immediate diagnosis, the newborns’ bodies rapidly were shutting down, and in each case, the parents were told they would likely lose their baby.

With the parents consent, the newborns underwent rapid whole-genome sequencing (rWGS) to try and determine the cause of their symptoms. Leveraging Rady’s rWGS pipeline results were turned around in about a day. In each case, rWGS enabled the team at Rady’s to successfully identify a rare but treatable genetic disorder so the newborn could undergo targeted therapy to dramatically alter the course of the disease. The babies were able to be taken home from the NICU shortly after diagnosis, and are healthy and happy today.

Multiple technology partners power RCIGM’s workflow to deliver this rapid and life-changing diagnosis. The institute uses Illumina NovaSeq for 40x sequencing, followed by rapid alignment and variant calling with Edico Genome’s DRAGEN pipeline. Copy number variation (CNV) analysis is performed on DNAnexus and combined with the file from DRAGEN. The combined VCF is then uploaded to Fabric Genomics for interpretation and reporting. Together with their partners, RCIGM has reduced the WGS turnaround time from a few weeks to under 36 hours.

Throughout the conference, other organizations shared their success stories of whole genome or exome sequencing for rapid diagnosis in newborns. Speakers also made a financial case for performing genomic sequencing on newborns, demonstrating that healthcare costs saved by a reduced length of hospitalization and ongoing care add up to more than the investment for sequencing. It is possible to save lives without increasing costs, a win-win for everyone.   

Hearing case study after case study of successful and rapid diagnosis with genomic sequencing in newborns drove home the message that the medical community is seeing concrete value in investing in rWGS. Further, as sequencing and bioinformatics technology continues to improve, physicians will have earlier access to genomic information to inform treatment decisions. As rWGS continues to gain momentum, genomic testing can become more universally available so newborns and their families can get the right diagnosis and the right treatment in time.

Integrating Multiple Data Sources to Power Discovery and Analysis

Precision Medicine World Conference (PMWC) took place in January in Mountain View, California, and offered attendees the opportunity to learn about innovative technologies, initiatives, and clinical case studies that are catalyzing the adoption of precision medicine in the clinic. DNAnexus was pleased to host a panel to discuss scalable infrastructure/platforms integrating next-generation sequencing (NGS) and other data (e.g. phenotypic) to power discovery and analysis in pharma and the clinic. Learn more below and watch the panel discussion.

Moderator: DNAnexus, Brady Davis, Chief Strategy Officer

 

Panelists:
AstraZeneca/MedImmune – David Fenstermacher, VP BioInformatics

Sutter Health – Greg Tranah,  Director, CPMC Research Institute, Adjunct Professor Dept. of Epidemiology & Biostatistics, UCSF

 Carol Franc Buck Breast Cancer Center at UCSF– Laura Esserman, Director

City of Hope – Sorena Nadaf, SVP & CIO

 

Abstract:

Health care providers increasingly require multi-omic datasets, including phenotypic data informed by genomic data. Such data needs to be obtained in an economically sustainable way and made available on an agile user-friendly platform so that these data may inform clinical care and lead to health improvements.

Pharmaceutical companies are interested in obtaining datasets containing phenotypic/clinical and genomic information generated from patient cohorts of specific disease areas. Such datasets can help pharma researchers identify drug targets or find biomarkers, validate hypotheses related to the interaction of genomics with disease or with specific therapies, and identify candidate populations for future clinical trials. Payers are also interested in the outcomes related to new discoveries and therapies in order to reimburse for these treatments.

This discussion focuses on how healthcare provider organizations, pharmas and payers are working toward solving these complex and challenging problems from a technical and business model perspective.

 

 

Benchmark and Advance Computational Methods for Targeted Strain Detection

The second Mosaic Community Challenge: Strains #2 is now live! 

In order to develop biotherapeutic products that are based on live strains of commensal bacteria, we need to be able to accurately detect and track how these product strains perform in patients after they are administered. Being able to accurately detect specific strains, given that there may be closely related strains in the sample, is the first step towards characterization of biotherapeutic products in terms of their dosage and efficacy.

Strains Challenge #2 is a slightly different problem than the first Strains Challenge. Strains #1 is looking at advancing methods to profile a sample at the strain-level, whereas Strains #2 is a targeted study to track the presence of certain known strains in a sample. Learn more and sign up to participate here.

Webinar: Introduction to Strains #2 Challenge 

Date: Wednesday, February 21st
Time: 10:30am PST (1:30pm EST)

Join us for an introduction to the Strains #2 challenge, and hear the challenge sponsors discuss how you can participate and contribute to the improvement of strain-level microbial analysis.