Clinical OMICS

MAY-JUN 2019

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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www.clinicalomics.com May/June 2019 Clinical OMICs 39 T hanks to biobanks and large-scale, case-control studies such as Genome Wide Association Studies (GWAS), mil- lions of genetic variants have been linked to several complex diseases. When variants are combined in a polygenic risk score (PRS), they can potentially identify people at signifi- cantly increased genetic risk to develop a disease compared to the average population, allowing for personalization of preventive plans. "The problem is that genetic labs don't have the skills to perform genomic-prediction analysis pipeline based on polygenic risk score, because despite being a simple weighted sum of the alleles' effects, polygenic risk score is complex and computationally intensive to implement," Giordano Bottà, Ph.D., CEO and co-founder of Allelica, told Clinical OMICs. Bottà, a molecular biologist, joined two co-founders— geneticist George Busby, Ph.D., and software engineer Paolo Di Domenico—to launch Allelica in January 2018. Allelica is a Rome-based provider of risk prediction and GWAS anal- ysis services to researchers and biobanks, with a focus on providing PRS for common disease quickly and accurately, using a cloud-based, software-as-a-service (SaaS) model. "Allelica built the in-cloud infrastructure to analyze large genomics data in a seamlessly, fast, and safe way. Moreover, Allelica performs statistical analysis to identify the most predictive set of variants and validate their pre- dictive power on the UK Biobank," Bottà added. "We built polygenic risk score that can identify people at more than three-fold risk of developing complex diseases compared to the average population, and we provide advanced models including covariates such as age, family history, and tradi- tional risk factors." Allelica says its analysis com- bines its review of genetic risk with lifestyle and clinical factors. To read DNA, the company uses Illumina's Infinium Global Screening Array scan- ning systems, which are designed to allow the genotyping of more than 750,000 genetic variants with an accu- racy greater than 99.9 percent. A ntibiotic resistance has long been recognized as a top global health threat. It causes more than 2 million infec- tions and 23,000 deaths per year in the U.S., according to the Centers for Disease Control and Prevention. Day Zero Diagnostics (DZD), based at the Pagliuca Har- vard Life Lab, is developing one solution to this threat—a rapid, whole-genome sequencing (WGS)-based diagnostic designed to identify the species and antibiotic resistance profile of a bacterial infection within hours. "Our primary development program is focused on cre- ating a rapid diagnostic for sepsis that can provide both species ID and comprehensive antibiotic resistance profiles so physicians can use targeted antibiotics at the first oppor- tunity," DZD President and CEO Jong Lee, a co-founder of the company, said. "We also provide a WGS-based rapid response service to help hospital infection control teams more effectively address suspected nosocomial infections." DZD was founded in 2016 by researchers from Har- vard and Massachusetts General Hospital. In January, DZD completed an $8.6 million Series A financing led by healthcare-focused venture capital firm Triventures, with additional funding from Sands Capital Ventures and Golden Seeds. The proceeds will enable DZD to accelerate develop- ment of its computational approach and Blood2Bac sam- ple preparation technology, designed to isolate and enrich for bacterial DNA at high sensitivity directly from com- plex clinical samples containing over a billion times more human DNA. One approach is called Keynome, a machine learning algorithm designed to predict the antibiotic resistance profiles of pathogens based on their genomic sequences. Keynome is being developed and trained on MicrohmDB, DZD's proprietary database containing what the company said is one of the largest collections of patho- gen genomic sequences, combined with their known phe- notypic resistance profiles. "Our work on nosocomial infections has led to the cre- ation of new capabilities for automated detection of out- breaks from genomic data," Lee added. JONG LEE President and CEO, Day Zero Diagnostics GIORDANO BOTTÀ CEO and co-founder, Allelica bestbrk / iStock / Getty Images

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