Johns Hopkins All Children's Research

Genomics Core

Our Genomics Core is devoted to genomics research and offers a variety of services to researchers, clinicians and physicians. 

The Johns Hopkins All Children’s Genomics Core offers a wide range of genomics services, including quality control (QC) of nucleic acids and custom next-generation sequencing (NGS) assays, such as Illumina TSCA, Ampliseq, HaloPlex and SureSelect.

Our Genomics Core is devoted to genomics research and aims to understand the structure and regulation of the genome, including the mapping of genes and sequencing of DNA and their transcripts. We also examine molecular mechanisms and genetic and environmental factors in diseases.

Our Genomics Core collaborates with Johns Hopkins University. These combined resources provide some of the most advanced infrastructure for genomics research in the nation. Our team serves academic and industry leaders from a variety of disciplines and backgrounds and supports the various needs of researchers, clinicians and physicians.

Next-Generation Sequencing

Our core provides NGS solutions for any project size and type with the use of Illumina’s advanced sequencing by synthesis (SBS) technology. The use of NGS technology can help identify potential biomarkers for fast and noninvasive patient tests as well as therapeutic targets. The Illumina platform allows for varying read lengths and run types that can generate high-quality data in as few as seven hours. Some of our NGS services include:

  • 16S rRNA Metagenomics Sequencing  
  • ChIP-Seq
  • Custom assays (Illumina TSCA, AmpliSeq, HaloPlex, SureSelect)   
  • de novo sequencing
  • DNA methylation  
  • DNA sequencing 
  • Low Level RNA/DNA detection 
  • RNA sequencing
    • mRNA-sequencing
    • Ribosome footprint profiling
    • Small RNA sequencing
    • Whole transcriptome 
  • Single-cell sequencing  
  • Whole genome exome sequencing

Our Technology

The Johns Hopkins All Children’s Genomics Core uses a variety of technology, including:

10x Chromium Controller

The 10x Chromium Controller allows us to prepare sequencing libraries for single cell analysis. Some of the current single cell assays are assay for transposase-accessible chromatin (ATAC), copy-number variation (CNV), exome and methylation, gene expression, immune profiling and whole genome sequencing (WGS).

Agilent 2100 Bioanalyzer

The 2100 Bioanalyzer instrument, together with the 2100 Expert Software, provides highly precise analytical evaluation of various samples types in many workflows.

Bio-Rad QX100 Droplet Digital PCR System

The Bio-Rad QX100 Droplet Digital PCR System provides an absolute quantification of target DNA or RNA molecules that is much more sensitive than standard qPCR instruments. This system offers a variety of applications including detection of low expressed mutations, rare sequences and transcripts.

Covaris Sonicator

The Covaris Focus Ultrasonicator is a single tube system developed for high-performance sample shearing using adaptive focused acoustic energy.

Droplet Digital PCR

Droplet Digital PCR is a method that is based on water-oil emulsion droplet technology and provides ultrasensitive and absolute nucleic acid quantification. It is useful for low-abundance targets, targets in complex backgrounds, allelic variants (SNPs) and for monitoring subtle changes in target levels that cannot be detected with real-time PCR.

Eppendorf epMotion M5073

The epMotion allows automation of routine pipetting tasks in the lab, eliminates manual pipetting errors and maximizes the reproducibility of assays.

Illumina HiSeq 2500

The HiSeq 2500 is ideal for large scale projects including single cell-seq, ATAC-seq, methyl-seq, whole transcriptome sequencing, whole genome sequencing and much more.

Illumina MiSeq

The Illumina MiSeq is ideal for small projects such as targeted sequencing assays, small genome sequencing and 16S metagenomics sequencing.

Illumina NextSeq 550

The Illumina NextSeq 550 is ideal for mid-size projects including RNA-seq, ChIP-seq, mRNA-seq, exome-seq, and whole genome sequencing.

LifeTech Quant Studio 7 Flex qPCR instrument

The QuantStudio 7 Flex System has been optimized to enable the broadest range of quantitative PCR applications, with additional dyes and format options.

Pippin Prep DNA Fractionator

The platform features the ability to collect narrow and even fragment distributions, as well as the flexibility to collect wide ranges of fragments in place of using gels.

Qubit Fluorometer

The Qubit Fluorometer accurately measure DNA, RNA, and protein quantity using fluorescent dyes that are specific to the target of interest.

Meet Our Expert

John Marchica 

John Marchica  Senior Research Specialist 

John is a senior genomics research specialist II at Johns Hopkins All Children’s Hospital. He joined the hospital staff in 2018 and established the Genomics Core. John manages daily operations and maintains and operates the Illumina sequencers (MiSeq, NextSeq 550 and HiSeq 2500). His specialties include molecular biology techniques, next-generation sequencing library preparations/assay development, cell culture and project/lab management. Before joining Johns Hopkins All Children’s, John was a research specialist at Sanford Burnham Prebys Medical Discovery Institute in Orlando, Florida. He earned his Bachelor of Science in Biochemistry from Stony Brook University in Stony Brook, New York. 

We want to work with you.

The Johns Hopkins All Children’s Genomics Core offers a wide range of genomics services and supports the various needs of researchers, clinicians and physicians. Please fill out our contact form and leave a brief description of your project. Once submitted, we will contact you to set up a meeting.