ABSTRACT
Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.
Subject(s)
Haplotypes/genetics , High-Throughput Nucleotide Sequencing/methods , Neoplasms/genetics , Sequence Analysis, DNA/methods , DNA/genetics , Genome, Human , Genomic Structural Variation , Germ Cells , Humans , Nucleic Acid Conformation , Oncogene Proteins, Fusion/genetics , Polymorphism, Single NucleotideABSTRACT
This study describes the synthesis of five novel C2-symmetric organocatalysts that facilitate the on-water asymmetric aldol reaction at low catalyst loading (1 mol%) without the use of additives. Each catalyst is composed of two diprolinamide units joined by a symmetric alkyl bridging group allowing for systematic modulation of catalytic site proximity. Typically, catalysts in this manuscript which bear the catalytic units in close proximity gave the best reaction outcomes in terms of conversion (up to >99%), diastereomeric ratio (4/96, syn/anti) and enantiomeric excess (up to 97%). This effect has been attributed to the assembly of a chiral pocket, facilitated by hydrogen bonding at the oil-in-water interface.
ABSTRACT
Saturated aqueous solutions of various common salts were examined for their effect on aqueous aldol reactions catalysted by a highly active C(2)-symmetric diprolinamide organocatalyst developed in our laboratory. With respect to the aldol reaction between cyclohexanone and 4-nitrobenzaldehyde, deionised water was always a superior medium to salt solutions though some correlation to increasing anion size and depression in enantiomeric excess could be observed. Additionally, the complete inhibition of catalyst activity observed when employing tap water could be alleviated by the inclusion of ethylenediaminetetraacetate (EDTA) into the aqueous media prior to reaction initiation. Extension of these reaction conditions demonstrated that these ionic effects vary on a case-to-case basis depending on the ketone/aldehyde combination.
