Curt Scharfe, MD, PhD, FACMG

1. Improving Genetic Disease Screening:

Genetic disease screening programs require improved genomic and analytical tools to increase accuracy and reduce false-positive results. Much of our work focuses on newborn screening (NBS), where we develop short- and long-read genomic sequencing methods and targeted metabolomics assays for use with dried blood spots. Screening data are analyzed using Random Forest machine learning models to improve detection of metabolic and genetic disorders included on the Recommended Uniform Screening Panel (RUSP).

A second major focus of our work is understanding biological, demographic, and technical sources of variability in newborn screening. We have shown that birth weight, gestational age, sex, maternal factors, ancestry, and timing of specimen collection shortly after birth significantly influence levels of disease-associated biomarkers in blood. To support population-scale analysis and interpretation, we developed dbRUSP, a web-based, interactive database of screening results from more than half a million babies reported by a public newborn screening program. By defining how these variables affect screening performance, our work supports more precise interpretation of results and improved population-level accuracy.

• Improving newborn screening accuracy through genome sequencing, targeted metabolomics, and machine learning
• Association of Maternal Age and Blood Markers for Metabolic Disease in Newborns
• Validation of a targeted metabolomics panel for improved second-tier newborn screening
• dbRUSP: An Interactive Database to Investigate Inborn Metabolic Differences for Improved Genetic Disease Screening
• Ethnic Variability in Newborn Metabolic Screening Markers Associated With False-Positive Outcomes
• Reducing False-Positive Results in Newborn Screening Using Machine Learning
• Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia
• Elevated methylmalonic acidemia (MMA) screening markers in Hispanic and preterm newborns
• Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis
• Timing of Newborn Blood Collection Alters Metabolic Disease Screening Performance
• Metabolic diversity in human populations and correlation with genetic and ancestral geographic distances
• CFTR haplotype phasing using long-read genome sequencing from ultra-low input DNA
• NBSTRN Tools to Advance Newborn Screening Research and Support Newborn Screening Stakeholders

2. Rapid Genotyping to Improve Patient Care:

Our laboratory develops rapid genotyping technologies that shorten the time from sample collection to molecular result. We pioneered an electronic, allele-specific detection platform that combines rapid PCR amplification with electrical sensing of DNA fragments. This work includes foundational methods development in impedance-based nucleic acid detection and has resulted in patent-pending technologies adaptable across genomic targets.

As a clinical proof-of-concept, we applied this platform to transthyretin (TTR) cardiac amyloidosis to address slow turnaround times of conventional genetic testing. The assay enables point-of-care detection of the pathogenic TTR V142I (c.424G>A) variant in less than 30 minutes from a fingerstick sample in individuals with congestive heart failure (CHF). This pathogenic founder variant is relatively common in individuals of West African ancestry and is often underrecognized due to variable penetrance and limited access to affordable, noninvasive testing.

• Allele-specific electrical genotyping for diagnosis of transthyretin amyloidosis
• Multi-frequency impedance sensing for detection and sizing of DNA fragments
• Validation of a rapid TTR genotyping assay as a point-of-care tool for cardiac amyloidosis diagnosis in low-income settings (PB1707)
• Enrichment for Cases of African-American Patients with Pathogenic TTR V142I Variant in the TOPCAT Trial

--> Demonstrative videos (Youtube):

Rapid Genotyping (het)

Watch the video

Presented by the Scharfe Lab at Yale University.

Song: "Sappheiros - Embrace [Chill]" is under a Creative Commons license (CC BY 3.0) Music promoted by BreakingCopyright: http://bit.ly/Sappheiros-Embrace

Rapid Genotyping (hom)

Watch the video

Presented by the Scharfe Lab at Yale University.

Song: "Sappheiros - Embrace [Chill]" is under a Creative Commons license (CC BY 3.0) Music promoted by BreakingCopyright: http://bit.ly/Sappheiros-Embrace

3. Multiplex Microhaplotype Sequencing:

Microhaplotypes (microhaps, MHs) are short genomic regions containing multiple closely spaced single nucleotide polymorphisms (SNPs) that provide highly informative, phase-resolved genetic markers. Broader adoption of microhaplotypes in forensic and population genetics requires scalable sequencing methods and standardized analytical tools. In collaboration with the laboratory of Kenneth Kidd, our group developed a 90-locus multiplex microhaplotype sequencing assay (mMHseq) enabled by our patented multiplex PCR methods for ultra-low DNA input. This technology supports reliable amplification from minimal or degraded samples, a key requirement in forensic applications. We also developed open-source, web-based software for visualization and interpretation of microhaplotype phase data. Together, these tools support mixture deconvolution, biogeographic ancestry estimation, and optimized panel design for forensic casework.

• Validation of novel forensic DNA markers using multiplex microhaplotype sequencing
• The population genetics characteristics of a 90 locus panel of microhaplotypes.
• A multipurpose panel of microhaplotypes for use with STR markers in casework

4. Multiplex Pathogen Detection:

Rapid and comprehensive pathogen detection is critical in transplant medicine and emerging infectious disease settings. Our laboratory developed a multiplex viral sequencing assay (mVseq) capable of simultaneously detecting 20 DNA viruses from small clinical samples, enabling broad-spectrum surveillance in immunocompromised patients. In response to the COVID-19 pandemic, we further developed a two-pronged strategy for rapid and high-throughput SARS-CoV-2 nucleic acid testing. This approach utilized multiplex reverse transcriptase PCR (m-RT-PCR) to amplify multiple viral genomic regions and a human control gene in a single-tube reaction directly from clinical samples without RNA extraction. Building on our expertise in electrical DNA detection, we also contributed to development of a label-free pathogen detection platform combining isothermal amplification with impedance-based sensing of self-assembled DNA nanoballs. This system enables rapid, low-cost, and highly sensitive nucleic acid detection adaptable across viral and bacterial targets.

• Transplant Virus Detection Using Multiplex Targeted Sequencing
• A two-pronged approach for rapid and high-throughput SARS-CoV-2 nucleic acid testing
• Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs

5. Mitochondrial Systems Biology and Gene Discovery:

A major focus of Dr. Scharfe’s research has been the discovery and characterization of nuclear-encoded mitochondrial proteins and their roles in human disease. Using functional genomics and proteomics in yeast, he helped identify hundreds of previously unrecognized mitochondrial proteins and demonstrated the value of cross-species screening for human disease gene discovery. To enable detection of pathogenic variants in patients with rare mitochondrial disorders, his group developed multiplex gene sequencing technologies to systematically analyze mitochondrial DNA and nuclear-encoded mitochondrial genes. He also pioneered mitochondrial systems and phenome-based approaches to study these diseases in the context of gene network perturbations rather than isolated gene defects. This work established genomic and systems-level frameworks that continue to inform rare disease gene discovery and diagnostic strategies.

• Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing
• Mapping gene associations in human mitochondria using clinical disease phenotypes
• Integrative analysis of the mitochondrial proteome in yeast
• Systematic screen for human disease genes in yeast