Nahum Smith
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View article: Editing stem cell genomes at scale to measure variant effects in diverse cell and genetic contexts
Editing stem cell genomes at scale to measure variant effects in diverse cell and genetic contexts Open
Multiplexed assays of variant effect (MAVEs) systematically measure variant function but have been limited to cancer cell lines rather than disease-relevant cell types. We developed saturation genome editing in human iPSCs (iPSC-SGE) to in…
View article: Saturation genome editing of <i>BARD1</i> resolves VUS and provides insight into BRCA1-BARD1 tumor suppression
Saturation genome editing of <i>BARD1</i> resolves VUS and provides insight into BRCA1-BARD1 tumor suppression Open
BARD1 variants are associated with hereditary breast cancer and neuroblastoma, yet, 98% of missense variants remain variants of uncertain significance (VUS). We applied Saturation Genome Editing (SGE) to assess 8,818 SNVs and 2,097 3-base …
View article: Guide Cloning v1
Guide Cloning v1 Open
This protocol details guide cloning.
View article: Pre-Sequencing v1
Pre-Sequencing v1 Open
This protocol details the information about pre-sequencing.
View article: Saturation Genome Editing v1
Saturation Genome Editing v1 Open
This collection details the saturation genome editing workflow.
View article: Tissue culture v1
Tissue culture v1 Open
This protocol details the tissue culture.
View article: Library Cloning v1
Library Cloning v1 Open
This protocol details about the library cloning.
View article: Guide Cloning v1
Guide Cloning v1 Open
This protocol details the guide cloning.
View article: Design v1
Design v1 Open
This protocol details the design of the workflow.
View article: Multiplexed assay of variant effect reveals residues of functional importance in the BRCA1 coiled-coil and serine cluster domains
Multiplexed assay of variant effect reveals residues of functional importance in the BRCA1 coiled-coil and serine cluster domains Open
Delineating functionally normal variants from functionally abnormal variants in tumor suppressor proteins is critical for cancer surveillance, prognosis, and treatment options. BRCA1 is a protein that has many variants of uncertain signifi…
View article: DNA repair function scores for 2172 variants in the BRCA1 amino-terminus
DNA repair function scores for 2172 variants in the BRCA1 amino-terminus Open
Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus,…
View article: A multiplex, prime editing framework for identifying drug resistance variants at scale
A multiplex, prime editing framework for identifying drug resistance variants at scale Open
CRISPR-based genome editing has revolutionized functional genomics, enabling screens in which thousands of perturbations of either gene expression or primary genome sequence can be competitively assayed in single experiments. However, for …
View article: DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus
DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus Open
Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus,…
View article: SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing
SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing Open
Background The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic …
View article: SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing
SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing Open
Structured Abstract Background The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. C…
View article: Beyond Blood Smears: Qualification of Plasmodium 18S rRNA as a Biomarker for Controlled Human Malaria Infections
Beyond Blood Smears: Qualification of Plasmodium 18S rRNA as a Biomarker for Controlled Human Malaria Infections Open
18S rRNA is a biomarker that provides an alternative to thick blood smears in controlled human malaria infection (CHMI) trials. We reviewed data from CHMI trials at non-endemic sites that used blood smears and Plasmodium 18S rRNA/rDNA biom…
View article: Malaria Parasite Density in Individuals with Different Rapid Diagnostic Test Results and Concentrations of HRP2 Antigen
Malaria Parasite Density in Individuals with Different Rapid Diagnostic Test Results and Concentrations of HRP2 Antigen Open
Low-density malaria infections are a source of human morbidity in endemic settings and potentially contribute to ongoing malaria transmission. Conventional rapid diagnostic tests (RDTs) were designed to detect clinically relevant parasite …
View article: Screening for<i>Pfhrp2/3</i>-Deleted<i>Plasmodium falciparum</i>, Non-<i>falciparum</i>, and Low-Density Malaria Infections by a Multiplex Antigen Assay
Screening for<i>Pfhrp2/3</i>-Deleted<i>Plasmodium falciparum</i>, Non-<i>falciparum</i>, and Low-Density Malaria Infections by a Multiplex Antigen Assay Open
These are the first reports of Pfhrp2/3 deletion mutants in Angola. High-throughput multiplex antigen detection can inexpensively screen for low-density P. falciparum, non-falciparum, and Pfhrp2/3-deleted parasites to provide population-le…
View article: Accurate Pan-Cancer Molecular Diagnosis of Microsatellite Instability by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing
Accurate Pan-Cancer Molecular Diagnosis of Microsatellite Instability by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing Open
BACKGROUND Microsatellite instability (MSI) is an emerging actionable phenotype in oncology that informs tumor response to immune checkpoint pathway immunotherapy. However, there remains a need for MSI diagnostics that are low cost, highly…