Dina Zielinski

DNA Fountain enables a robust and efficient storage architecture

A reliable and efficient DNA storage architecture DNA has the potential to provide large-capacity information storage. However, current methods have only been able to use a fraction of the theoretical maximum. Erlich and Zielinski present a method, DNA Fountain, which approaches the theoretical maximum for information stored per nucleotide. They demonstrated efficient encoding of information—including a full computer operating system—into DNA that could be retrieved at scale after multiple rounds of polymerase chain reaction. Science, this issue p. 950 A resilient DNA storage strategy enables near-maximal information content per nucleotide. DNA is an attractive medium to store digital information. Here we report a storage strategy, called DNA Fountain, that is highly robust and approaches the information capacity per nucleotide. Using our approach, we stored a full computer operating system, movie, and other files with a total of 2.14 × 106 bytes in DNA oligonucleotides and perfectly retrieved the information from a sequencing coverage equivalent to a single tile of Illumina sequencing. We also tested a process that can allow 2.18 × 1015 retrievals using the original DNA sample and were able to perfectly decode the data. Finally, we explored the limit of our architecture in terms of bytes per molecule and obtained a perfect retrieval from a density of 215 petabytes per gram of DNA, orders of magnitude higher than previous reports.

Genome-wide profiling of heritable and de novo STR variations

Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool.github.io/HipSTR.

OTX2 Duplication Is Implicated in Hemifacial Microsomia

Hemifacial microsomia (HFM) is the second most common facial anomaly after cleft lip and palate. The phenotype is highly variable and most cases are sporadic. We investigated the disorder in a large pedigree with five affected individuals spanning eight meioses. Whole-exome sequencing results indicated the absence of a pathogenic coding point mutation. A genome-wide survey of segmental variations identified a 1.3 Mb duplication of chromosome 14q22.3 in all affected individuals that was absent in more than 1000 chromosomes of ethnically matched controls. The duplication was absent in seven additional sporadic HFM cases, which is consistent with the known heterogeneity of the disorder. To find the critical gene in the duplicated region, we analyzed signatures of human craniofacial disease networks, mouse expression data, and predictions of dosage sensitivity. All of these approaches implicated OTX2 as the most likely causal gene. Moreover, OTX2 is a known oncogenic driver in medulloblastoma, a condition that was diagnosed in the proband during the course of the study. Our findings suggest a role for OTX2 dosage sensitivity in human craniofacial development and raise the possibility of a shared etiology between a subtype of hemifacial microsomia and medulloblastoma.

Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach

Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next-generation sequencing to allow such large-scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large-scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost-effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.

Back to the family: a renewed approach to rare variant studies

A report on the 62nd Annual Meeting of the American Society of Human Genetics, San Francisco, California, USA, 6-10 November 2012.

Capacity-approaching DNA storage

DNA is an attractive medium to store digital information. Here, we report a storage strategy, called DNA Fountain, that is highly robust and approaches the information capacity per nucleotide. Using our approach, we stored a full computer operating system, movie, and other files with a total of 2.14 × 106 bytes in DNA oligos and perfectly retrieved the information from a sequencing coverage equivalent of a single tile of Illumina sequencing. We also tested a process that can allow 2.18 × 1015 retrievals using the original DNA sample and were able to perfectly decode the data. Finally, we explored the limit of our architecture in terms of bytes per molecules and obtained a perfect retrieval from a density of 215Petabyte/gram of DNA, orders of magnitudes higher than previous techniques.Humanity produces data at exponential rates, creating a growing demand for better storage devices. DNA molecules are an attractive medium to store digital information due to their durability and high information density. Recent studies have made large strides in developing DNA storage schemes by exploiting the advent of massive parallel synthesis of DNA oligos and the high throughput of sequencing platforms. However, most of these experiments reported small gaps and errors in the retrieved information. Here, we report a strategy to store and retrieve DNA information that is robust and approaches the theoretical maximum of information that can be stored per nucleotide. The success of our strategy lies in careful adaption of recent developments in coding theory to the domain specific constrains of DNA storage. To test our strategy, we stored an entire computer operating system, a movie, a gift card, and other computer files with a total of 2.14*10^6 bytes in DNA oligos. We were able to fully retrieve the information without a single error even with a sequencing throughput on the scale of a single tile of an Illumina sequencing flow cell. To further stress our strategy, we created a deep copy of the data by PCR amplifying the oligo pool in a total of nine successive reactions, reflecting one complete path of an exponential process to copy the file 218*10^12 times. We perfectly retrieved the original data with only five million reads. Taken together, our approach opens the possibility of highly reliable DNA-based storage that approaches the information capacity of DNA molecules and enables virtually unlimited data retrieval.

DNA.Land: A Digital Biobank Using A Massive Crowdsourcing Approach

Precision medicine necessitates large scale collections of genomes and phenomes. Despite decreases in the costs of genomic technologies, collecting these types of information at scale is still a daunting task that poses logistical challenges and requires consortium-scale resources. Here, we describe DNA.Land, a digital biobank to collect genome and phenomes with a fraction of the resources of traditional studies at the same scale. Our approach relies on crowd-sourcing data from the rapidly growing number of individuals that have access to their own genomic datasets through Direct-to-Consumer (DTC) companies. To recruit participants, we developed a series of automatic return-of-results features in DNA.Land that increase users’ engagement while stratifying human subject research protection. So far, DNA.Land has collected over 43,000 genomes in 20 months of operation, orders of magnitude higher than previous digital attempts by academic groups. We report lessons learned in running a digital biobank, our technical framework, and our approach regarding ethical, legal, and social implications.

Biological screens from linear codes: theory and tools

Molecular biology increasingly relies on large screens where enormous numbers of specimens are systematically assayed in the search for a particular, rare outcome. These screens include the systematic testing of small molecules for potential drugs and testing the association between genetic variation and a phenotype of interest. While these screens are “hypothesis-free,” they can be wasteful; pooling the specimens and then testing the pools is more efficient. We articulate in precise mathematical ways the type of structures useful in combinatorial pooling designs so as to eliminate waste, to provide light weight, flexible, and modular designs. We show that Reed-Solomon codes, and more generally linear codes, satisfy all of these mathematical properties. We further demonstrate the power of this technique with Reed-Solomonbased biological experiments. We provide general purpose tools for experimentalists to construct and carry out practical pooling designs with rigorous guarantees for large screens.

OTX2 Dosage Sensitivity is Implicated in Hemifacial Microsomia

Hemifacial microsomia (HFM) is the second most common facial anomaly after cleft lip and palate. The phenotype is highly variable and most cases are sporadic. Here, we investigated the disorder in a large pedigree with five affected individuals spanning eight meioses. We performed whole-exome sequencing and a genome-wide survey of segmental variations. Analysis of the exome sequencing results indicated the absence of a pathogenic coding point mutation. Inspection of segmental variations identified a 1.3Mb duplication of chromosome 14q22.3 in all affected individuals that was absent in more than 1000 chromosomes of ethnically matched controls. The duplication was absent in seven additional sporadic HFM cases, which is concordant with the known heterogeneity of the disorder. To find the critical gene in the duplicated region, we analyzed signatures of human craniofacial disease networks, mouse expression data, and predictions of dosage sensitivity. All of these approaches implicated OTX2 as the most likely causal gene. Moreover, OTX2 is a known oncogenic driver in medulloblastoma, a condition that was diagnosed in the proband during the course of our study. Our findings highlight dosage sensitivity of OTX2 in human craniofacial development and suggest a possible shared etiology between a subtype of hemifacial microsomia and medulloblastoma.