June 1, 2021  |  

Building a platinum human genome assembly from single haplotype human genomes generated from long molecule sequencing

The human reference sequence has provided a foundation for studies of genome structure, human variation, evolutionary biology, and disease. At the time the reference was originally completed there were some loci recalcitrant to closure; however, the degree to which structural variation and diversity affected our ability to produce a representative genome sequence at these loci was still unknown. Many of these regions in the genome are associated with large, repetitive sequences and exhibit complex allelic diversity such producing a single, haploid representation is not possible. To overcome this challenge, we have sequenced DNA from two hydatidiform moles (CHM1 and CHM13), which are essentially haploid. CHM13 was sequenced with the latest PacBio technology (P6-C5) to 52X genome coverage and assembled using Daligner and Falcon v0.2 (GCA_000983455.1, CHM13_1.1). Compared to the first mole (CHM1) PacBio assembly (GCA_001007805.1, 54X) contig N50 of 4.5Mb, the contig N50 of CHM13_1.1 is almost 13Mb, and there is a 13-fold reduction in the number of contigs. This demonstrates the improved contiguity of sequence generated with the new chemistry. We annotated 50,188 RefSeq transcripts of which only 0.63% were split transcripts, and the repetitive and segmental duplication content was within the expected range. These data all indicate an extremely high quality assembly. Additionally, we sequenced CHM13 DNA using Illumina SBS technology to 60X coverage, aligned these reads to the GRCh37, GRCh38, and CHM13_1.1 assemblies and performed variant calling using the SpeedSeq pipeline. The number of single nucleotide variants (SNV) and indels was comparable between GRCh37 and GRCh38. Regions that showed increased SNV density in GRCh38 compared to GRCh37 could be attributed to the addition of centromeric alpha satellite sequence to the reference assembly. Alternatively, regions of decreased SNV density in GRCh38 were concentrated in regions that were improved from BAC based sequencing of CHM1 such as 1p12 and 1q21 containing the SRGAP2 gene family. The alignment of PacBio reads to GRCh37 and GRCh38 assemblies allowed us to resolve complex loci such as the MHC region where the best alignment was to the DBB (A2-B57-DR7) haplotype. Finally, we will discuss how combining the two high quality mole assemblies can be used for benchmarking and novel bioinformatics tool development.


June 1, 2021  |  

The resurgence of reference quality genome

Several new 3rd generation long-range DNA sequencing and mapping technologies have recently become available that are starting to create a resurgence in genome sequence quality. Unlike their 2nd generation, shortread counterparts that can resolve a few hundred or a few thousand basepairs, the new technologies can routinely sequence 10,000 bp reads or map across 100,000 bp molecules. The substantially greater lengths are being used to enhance a number of important problems in genomics and medicine, including de novo genome assembly, structural variation detection, and haplotype phasing. Here we discuss the capabilities of the latest technologies, and show how they will improve the “3Cs of Genome Assembly”: the contiguity, completeness, and correctness. We derive this analysis from (1) a metaanalysis of the currently available 3rd generation genome assemblies, (2) a retrospective analysis of the evolution of the reference human genome, and (3) extensive simulations with dozens of species across the tree of life. We also propose a model using support vector regression (SVR) that predicts genome assembly performance using four features: read lengths(L) and coverage values(C) that can be used for evaluating potential technologies along with genome size(G) and repeats(R) that present species specific characteristics. The proposed model significantly improves genome assembly performance prediction by adopting data-driven approach and addressing limitations of the previous hypothesis-driven methodology. Overall, we anticipate these technologies unlock the genomic “dark matter”, and provide many new insights into evolution, agriculture, and human diseases.


June 1, 2021  |  

Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements

Transmission of arboviruses such as Dengue Virus by Aedes aegypti causes debilitating disease across the globe. Disease in humans can include severe acute symptoms such as hemorrhagic fever and organ failure, but mosquitoes tolerate high titers of virus in a persistent infection. The mechanisms responsible for this viral tolerance are unclear. Recent publications highlighted the integration of genetic material from non-retroviral RNA viruses into the genome of the host during infection that relies upon endogenous retro-transcriptase activity from transposons. These endogenous viral elements (EVEs) found in the genome are predicted to be ancient, and at least some EVEs are under purifying selection, suggesting they are beneficial to the host. To characterize EVE biogenesis in a tractable system, we sequenced the Ae. aegypti cell line, Aag2, to 58-fold coverage and present a de novo assembly of the genome. The assembly contains 1.7 Gb of genomic and 255 Mb of alternative haplotype specific sequence, consisting of contigs with a N50 of 1.4 Mb; a value that, when compared with other assemblies of the Aedes genus, is from 1-3 orders of magnitude longer. The Aag2 genome is highly repetitive (70%), most of which is classified as transposable elements (60%). We identify EVEs in the genome homologous to a range of extant viruses, many of which cluster in these regions of repetitive DNA. The contiguous assembly allows for more comprehensive identification of the transposable elements and EVEs that are most likely to be lost in assemblies lacking the read length of SMRT Sequencing.


June 1, 2021  |  

From Sequencing to Chromosomes: New de novo assembly and scaffolding methods improve the goat reference genome

Single-molecule sequencing is now routinely used to assemble complete, high-quality microbial genomes, but these assembly methods have not scaled well to large genomes. To address this problem, we previously introduced the MinHash Alignment Process (MHAP) for overlapping single-molecule reads using probabilistic, locality-sensitive hashing. Integrating MHAP with Celera Assembler (CA) has enabled reference-grade assemblies of model organisms, revealing novel heterochromatic sequences and filling low-complexity gap sequences in the GRCh38 human reference genome. We have applied our methods to assemble the San Clemente goat genome. Combining single-molecule sequencing from Pacific Biosciences and BioNano Genomics generates and assembly that is over 150-fold more contiguous than the latest Capra hircus reference. In combination with Hi-C sequencing, the assembly surpasses reference assemblies, de novo, with minimal manual intervention. The autosomes are each assembled into a single scaffold. Our assembly provides a more complete gene reconstruction, better alignments with Goat 52k chip, and improved allosome reconstruction. In addition to providing increased continuity of sequence, our assembly achieves a higher BUSCO completion score (84%) than the existing goat reference assembly suggesting better quality annotation of gene models. Our results demonstrate that single-molecule sequencing can produce near-complete eukaryotic genomes at modest cost and minimal manual effort.


June 1, 2021  |  

Comparative Studies of Mammalian Sex Chromosomes: From Cytogenetics to NGS

It is a common knowledge that sex chromosome mutations are better tolerated and more viable compared to changes in autosomes. This is explained by relatively low gene density in both the X and the Y chromosome and by random X chromosome inactivation in mammalian females buffering the effect of X-aneuploidies. However, it is not well understood why apparently similar sex chromosome abnormalities, such as X-monosomy or certain Y chromosome rearrangements, result in different phenotypic effects in different species. It is thought that this is due to species differences in the organization of the Y chromosome, differences in the set of genes escaping X-inactivation, and the presence of species/lineage specific sex-linked genes with functions in development and reproduction. Current knowledge about the species differences in sex chromosome organization and function is limited, this despite the availability of reference genome assemblies for most domestic species. It appears that sequence assembly of the X chromosome in most species is rather patchy containing multiple gaps and possible misassemblies, being the poorest in the pseudoautosomal region and in regions containing putative lineage-specific sequences. The Y chromosome, on the other hand, is typically not included in the reference genome and is studied separately, whereas complete sequence assembly of the male-specific portion of the Y is not yet available for any domestic species. In this talk I will discuss comparative organization and function of animal sex chromosomes and related phenotypes proceeding from our research in horses.


June 1, 2021  |  

MaSuRCA Mega-Reads Assembly Technique for haplotype resolved genome assembly of hybrid PacBio and Illumina Data

The developments in DNA sequencing technology over the past several years have enabled large number of scientists to obtain sequences for the genomes of their interest at a fairly low cost. Illumina Sequencing was the dominant whole genome sequencing technology over the past few years due to its low cost. The Illumina reads are short (up to 300bp) and thus most of those draft genomes produced from Illumina data are very fragmented which limits their usability in practical scenarios. Longer reads are needed for more contiguous genomes. Recently Pacbio sequencing made significant advances in developing cost-effective long-read (>10000bp) sequencing technology and their data, although several times more expensive than Illumina, can be used to produce high quality genomes. Pacbio data can be used for de novo assembly, however due to its high error rate high coverage of the genome is required this raising the cost barrier. A solution for cost-effective genomes is to combine Pacbio and Illumina data leveraging the low error rates of the short Illumina reads and the length of the Pacbio reads. We have developed MaSuRCA mega-reads assembler for efficient assembly of hybrid data sets and we demonstrate that it performs well compared to the other published hybrid techniques. Another important benefit of the long reads is their ability to link the haplotype differences. The mega-reads approach corrects each Pacbio read independently and thus haplotype differences are preserved. Thus, leveraging the accuracy of the Illumina data and the length of the Pacbio reads, MaSuRCA mega-reads can produce haplotype-resolved genome assemblies, where each contig has sequence from a single haplotype. We present preliminary results on haplotype-resolved genome assemblies of faux (proof-of-concept) and real data.


June 1, 2021  |  

Diploid genome assembly and comprehensive haplotype sequence reconstruction

Outside of the simplest cases (haploid, bacteria, or inbreds), genomic information is not carried in a single reference per individual, but rather has higher ploidy (n=>2) for almost all organisms. The existence of two or more highly related sequences within an individual makes it extremely difficult to build high quality, highly contiguous genome assemblies from short DNA fragments. Based on the earlier work on a polyploidy aware assembler, FALCON ( https://github.com/PacificBiosciences/FALCON) , we developed new algorithms and software (“FALCON-unzip”) for de novo haplotype reconstructions from SMRT Sequencing data. We generate two datasets for developing the algorithms and the prototype software: (1) whole genome sequencing data from a highly repetitive diploid fungal (Clavicorona pyxidata) and (2) whole genome sequencing data from an F1 hybrid from two inbred Arabidopsis strains: Cvi-0 and Col-0. For the fungal genome, we achieved an N50 of 1.53 Mb (of the 1n assembly contigs) of the ~42 Mb 1n genome and an N50 of the haplotigs (haplotype specific contigs) of 872 kb from a 95X read length N50 ~16 kb dataset. We found that ~ 45% of the genome was highly heterozygous and ~55% of the genome was highly homozygous. We developed methods to assess the base-level accuracy and local haplotype phasing accuracy of the assembly with short-read data from the Illumina® platform. For the ArabidopsisF1 hybrid genome, we found that 80% of the genome could be separated into haplotigs. The long range accuracy of phasing haplotigs was evaluated by comparing them to the assemblies from the two inbred parental lines. We show that a more complete view of all haplotypes could provide useful biological insights through improved annotation, characterization of heterozygous variants of all sizes, and resolution of differential allele expression. The current Falcon-Unzip method will lead to understand how to solve more difficult polyploid genome assembly problems and improve the computational efficiency for large genome assemblies. Based on this work, we can develop a pipeline enabling routinely assemble diploid or polyploid genomes as haplotigs, representing a comprehensive view of the genomes that can be studied with the information at hand.


June 1, 2021  |  

Un-zipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive hapltotig assemblies

Outside of the simplest cases (haploid, bacteria, or inbreds), genomic information is not carried in a single reference per individual, but rather has higher ploidy (n=>2) for almost all organisms. The existence of two or more highly related sequences within an individual makes it extremely difficult to build high quality, highly contiguous genome assemblies from short DNA fragments. Based on the earlier work on a polyploidy aware assembler, FALCON (https://github.com/PacificBiosciences/FALCON), we developed new algorithms and software (FALCON-unzip) for de novo haplotype reconstructions from SMRT Sequencing data. We apply the algorithms and the prototype software for (1) a highly repetitive diploid fungal genome (Clavicorona pyxidata) and (2) an F1 hybrid from two inbred Arabidopsis strains: CVI-0 and COL-0. For the fungal genome, we achieved an N50 of 1.53 Mb (of the 1n assembly contigs) of the ~42 Mb 1n genome and an N50 of the haplotigs of 872 kb from a 95X read length N50 ~16 kb dataset. We found that ~ 45% of the genome was highly heterozygous and ~55% of the genome was highly homozygous. We developed methods to assess the base-level accuracy and local haplotype phasing accuracy of the assembly with short-read data from the Illumina platform. For the Arabidopsis F1 hybrid genome, we found that 80% of the genome could be separated into haplotigs. The long range accuracy of phasing haplotigs was evaluated by comparing them to the assemblies from the two inbred parental lines. We show that a more complete view of all haplotypes could provide useful biological insights through improved annotation, characterization of heterozygous variants of all sizes, and resolution of differential allele expression. Finally, we applied this method to WGS human data sets to demonstrate the potential for resolving complicated, medically-relevant genomic regions.


June 1, 2021  |  

Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements

Transmission of arboviruses such as Dengue and Zika viruses by Aedes aegypti causes widespread and debilitating disease across the globe. Disease in humans can include severe acute symptoms such as hemorrhagic fever, organ failure, and encephalitis; and yet, mosquitoes tolerate high titers of virus in a persistent infection. The mechanisms responsible for tolerance to viral infection in mosquitoes are still unclear. Recent publications have highlighted the integration of genetic material from non-retroviral RNA viruses into the genome of the host during infection that relies upon endogenous retro-transcriptase activity from transposons. These endogenous viral elements (EVEs) found in the genome are predicted to be ancient and at least some EVEs are under purifying selection, which suggests that they are beneficial to the host. In order characterize EVE biogenesis in a tractable system we sequenced the Ae. aegypti cell line, Aag2, to 58X coverage and here present a de novo assembly of the genome. The assembly consists of 1.7 Gb of genomic and 255 Mb of alternative haplotype specific sequence, made up of contigs with a N50 of 1.4 Mb; a value that, when compared with other assemblies of the Aedes genus, is from 1-3 orders of magnitude longer. The Aag2 genome is highly repetitive (70%), most of which is classified as transposable elements (60%). We identify a plethora of EVEs in the genome homologous to a diverse range of extant viruses, many of which cluster in these regions of highly repetitive DNA. The highly contiguous nature of this assembly allows for a more comprehensive identification of the transposable elements and EVEs that are most likely to be lost in assemblies lacking the read length of SMRT Sequencing. Transmission of arboviruses such as Dengue Virus by Aedes aegypti causes widespread and debilitating disease across the globe. Disease in humans can include severe acute symptoms such as hemorrhagic fever, organ failure, and encephalitis; and yet, mosquitoes tolerate high titers of virus in a persistent infection. The mechanisms responsible for tolerance to viral infection in mosquitoes are still unclear. Recent publications have highlighted the integration of genetic material from non-retroviral RNA viruses into the genome of the host during infection that relies upon endogenous retro-transcriptase activity from transposons. These endogenous viral elements (EVEs) found in the genome are predicted to be ancient and at least some EVEs are under purifying selection, which suggests that they are beneficial to the host. In order characterize EVE biogenesis in a tractable system we sequenced the Ae. aegypti cell line, Aag2, to 58X coverage and here present a de novo assembly of the genome. The assembly consists of 1.7 Gb of genomic and 255 Mb of alternative haplotype specific sequence, made up of contigs with a N50 of 1.4 Mb; a value that, when compared with other assemblies of the Aedes genus, is from 1-3 orders of magnitude longer. The Aag2 genome is highly repetitive (70%), most of which is classified as transposable elements (60%). We identify a plethora of EVEs in the genome homologous to a diverse range of extant viruses, many of which cluster in these regions of highly repetitive DNA. The highly contiguous nature of this assembly allows for a more comprehensive identification of the transposable elements and EVEs that are most likely to be lost in assemblies lacking the read length of SMRT Sequencing. Transmission of arboviruses such as Dengue Virus by Aedes aegypti causes widespread and debilitating disease across the globe. Disease in humans can include severe acute symptoms such as hemorrhagic fever, organ failure, and encephalitis; and yet, mosquitoes tolerate high titers of virus in a persistent infection. The mechanisms responsible for tolerance to viral infection in mosquitoes are still unclear.


June 1, 2021  |  

Immune regions are no longer incomprehensible with SMRT Sequencing

The complex immune regions of the genome, including MHC and KIR, contain large copy number variants (CNVs), a high density of genes, hyper-polymorphic gene alleles, and conserved extended haplotypes (CEH) with enormous linkage disequilibrium (LDs). This level of complexity and inherent biases of short-read sequencing make it challenging for extracting immune region haplotype information from reference-reliant, shotgun sequencing and GWAS methods. As NGS based genome and exome sequencing and SNP arrays have become a routine for population studies, numerous efforts are being made for developing software to extract and or impute the immune gene information from these datasets. Despite these efforts, the fine mapping of causal variants of immune genes for their well-documented association with cancer, drug-induced hypersensitivity and immune-related diseases, has been slower than expected. This has in many ways limited our understanding of the mechanisms leading to immune disease. In the present work, we demonstrate the advantages of long reads delivered by SMRT Sequencing for assembling complete haplotypes of MHC and KIR gene clusters, as well as calling correct genotypes of genes comprised within them. All the genotype information is detected at allele- level with full phasing information across SNP-poor regions. Genotypes were called correctly from targeted gene amplicons, haplotypes, as well as from a completely assembled 5 Mb contig of the MHC region from a de novo assembly of whole genome shotgun data. De novo analysis pipeline used in all these approaches allowed for reference-free analysis without imputation, a key for interrogation without prior knowledge about ethnic backgrounds. These methods are thus easily adoptable for previously uncharacterized human or non-human species.


June 1, 2021  |  

Targeted sequencing and chromosomal haplotype assembly using TLA and SMRT Sequencing

With the increasing availability of whole-genome sequencing, haplotype reconstruction of individual genomes, or haplotype assembly, remains unsolved. Like the de novo genome assembly problem, haplotype assembly is greatly simplified by having more long-range information. The Targeted Locus Amplification (TLA) technology from Cergentis has the unique capability of targeting a specific region of the genome using a single primer pair and yielding ~2 kb DNA circles that are comprised of ~500 bp fragments. Fragments from the same circle come from the same haplotype and follow an exponential decay in distance from the target region, with a span that reaches the multi-megabase range. Here, we apply TLA to the BRCA1 gene on NA12878 and then sequence the resulting 2 kb circles on a PacBio RS II. The multiple fragments per circle were iteratively mapped to hg19 and then haplotype assembled using HAPCUT. We show that the 80 kb length of BRCA1 is represented by a single haplotype block, which was validated against GIAB data. We then explored chromosomal-scale haplotype assembly by combining these data with whole genome shotgun PacBio long reads, and demonstrate haplotype blocks approaching the length of chromosome 17 on which BRCA1 lies. Finally, by performing TLA without the amplification step and size selecting for reads >5 kb to maximize the number of fragments per read, we target whole genome haplotype assembly across all chromosomes.


June 1, 2021  |  

Resolving KIR genotypes and haplotypes simultaneously using Single Molecule, Real-Time Sequencing

The killer immunoglobulin-like receptors (KIR) genes belong to the immunoglobulin superfamily and are widely studied due to the critical role they play in coordinating the innate immune response to infection and disease. Highly accurate, contiguous, long reads, like those generated by SMRT Sequencing, when combined with target-enrichment protocols, provide a straightforward strategy for generating complete de novo assembled KIR haplotypes. We have explored two different methods to capture the KIR region; one applying the use of fosmid clones and one using Nimblegen capture.


June 1, 2021  |  

Highly contiguous de novo human genome assembly and long-range haplotype phasing using SMRT Sequencing

The long reads, random error, and unbiased sampling of SMRT Sequencing enables high quality, de novo assembly of the human genome. PacBio long reads are capable of resolving genomic variations at all size scales, including SNPs, insertions, deletions, inversions, translocations, and repeat expansions, all of which are both important in understanding the genetic basis for human disease, and difficult to access via other technologies. In demonstration of this, we report a new high-quality, diploid-aware de novo assembly of Craig Venter’s well-studied genome.


June 1, 2021  |  

Multiplex target enrichment using barcoded multi-kilobase fragments and probe-based capture technologies

Target enrichment capture methods allow scientists to rapidly interrogate important genomic regions of interest for variant discovery, including SNPs, gene isoforms, and structural variation. Custom targeted sequencing panels are important for characterizing heterogeneous, complex diseases and uncovering the genetic basis of inherited traits with more uniform coverage when compared to PCR-based strategies. With the increasing availability of high-quality reference genomes, customized gene panels are readily designed with high specificity to capture genomic regions of interest, thus enabling scientists to expand their research scope from a single individual to larger cohort studies or population-wide investigations. Coupled with PacBio® long-read sequencing, these technologies can capture 5 kb fragments of genomic DNA (gDNA), which are useful for interrogating intronic, exonic, and regulatory regions, characterizing complex structural variations, distinguishing between gene duplications and pseudogenes, and interpreting variant haplotyes. In addition, SMRT® Sequencing offers the lowest GC-bias and can sequence through repetitive regions. We demonstrate the additional insights possible by using in-depth long read capture sequencing for key immunology, drug metabolizing, and disease causing genes such as HLA, filaggrin, and cancer associated genes.


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