Whole-exome sequencing
All protein-coding exons in one test. Used for unexplained disease, hereditary risk, and consumer health workups that need more than a 50-gene panel.
Next-generation sequencing
Read the regions that change the case.
NGS at Patient Test Solutions, Inc is a clinical service of this laboratory: library preparation, sequencing, and interpretation under one accession. That includes targeted panels, cell-free DNA, and consumer-relevant tests such as whole-exome sequencing.
The science
Targeted sequence, reported in a clinical frame.
Solid-tumor panels interrogate defined amplicon regions — a hotspot set of more than 50 genes, and dedicated breast, colorectal, and lung panels. Cell-free DNA libraries support plasma when tissue is scarce or the question is circulating nucleic acid.
Low-input chemistry (down to about 100 pg) is useful for small biopsies, depleted FFPE, and cfDNA. Typical library preparation is a few hours with limited hands-on time, then sequencing and review at this laboratory.
Consumer NGS
The tests people actually ask for.
Most consumer and wellness genomics does not require reading every base of the genome. It requires reading the parts that change health — first among them, the exome.
Whole-exome sequencing
About 1% of the DNA. About 85% of the mutations that matter.
The exome is the protein-coding portion of the genome — roughly 1% of human DNA. That small fraction is estimated to harbor about 85% of mutations with large effects on disease-related traits. Whole-exome sequencing (WES) reads those coding regions at high depth instead of spreading coverage across the other 99%.
That is why WES is one of the most common clinical and consumer NGS tests: it is efficient, cheaper than a full genome, and still captures the majority of known disease-causing change. NovaSeq is the instrument we use when an exome needs production-scale output; MiSeq remains the bench for smaller targeted sets.
The 1% / 85% figure is the standard statement in the genetics literature (Choi et al., Proc. Natl. Acad. Sci. USA, 2009: protein-coding genes are ~1% of the genome but harbor ~85% of mutations with large effects on disease-related traits).
Cancer and carrier panels
Focused NGS of BRCA and related genes, or carrier genes, when the question is already known. Faster and deeper on the genes that were ordered.
Genome when the 1% is not enough
Whole-genome sequencing reads non-coding DNA as well. Most consumer and first-line clinical questions are still answered in the exome. We sequence the genome when the case requires it.
Instruments
MiSeq and NovaSeq, used in this laboratory.
Both systems read DNA by Illumina sequencing-by-synthesis. We do not show product photography here. What follows is how each instrument is used, and the science behind the read.
MiSeq
A compact benchtop sequencer. Cluster generation, sequencing, and base calling happen on the same instrument. Output is on the order of 540 Mb to 15 Gb per run, with up to about 25 million single reads and paired-end lengths up to 2 × 300 bp. Run time is typically several hours to about two days, depending on kit and read length.
Illumina uses it for targeted gene sequencing, amplicon sequencing, small genomes, and 16S-style work. In this laboratory it is the instrument for focused amplicon panels and smaller targeted cases that do not need production-scale output.
NovaSeq
A high-throughput sequencer built for large data output. NovaSeq systems use patterned flow cells and sequencing-by-synthesis (standard SBS on NovaSeq 6000; XLEAP-SBS on the NovaSeq X series). Output is measured in terabases per run — far above a MiSeq — with billions of reads when a run is configured for depth or batching.
These systems are used for whole-genome and whole-exome work at scale, and for large targeted or cell-free DNA batches. In this laboratory NovaSeq is used when a hotspot panel, a batched set of libraries, or a cfDNA case needs more reads than a benchtop run provides.
The shared chemistry
Sequencing by synthesis
Both instruments detect bases the same way. DNA fragments are attached to a flow cell and amplified into clusters. In each cycle, a reversible-terminator fluorescent nucleotide is incorporated, the camera records the color, the terminator is cleaved, and the next base is added. Billions of clusters are read in parallel. Paired-end sequencing then reads the other end of each fragment, which helps map repeats and confirm variants.
MiSeq keeps that chemistry in a small, single-flow-cell box for rapid targeted work. NovaSeq scales the same idea with denser flow cells and higher throughput so many libraries, or deeper coverage, can be sequenced in one run.
| MiSeq | NovaSeq | |
|---|---|---|
| Class | Benchtop, single flow cell | Production-scale, high-throughput |
| Chemistry | Illumina SBS, reversible terminators | Illumina SBS; XLEAP-SBS on NovaSeq X series |
| Typical output | ~540 Mb–15 Gb per run | Terabases per run (system- and flow-cell-dependent) |
| Reads (order of magnitude) | ~1–25 million single reads | Billions of reads per run |
| Max read length (published) | 2 × 300 bp | 2 × 250 bp (6000) / 2 × 300 bp (X series) |
| How we use it | Focused amplicon and smaller targeted panels | Batched panels, broader hotspot sets, cfDNA when more depth is required |
Specifications summarized from Illumina’s published MiSeq and NovaSeq documentation. MiSeq, NovaSeq, SBS, and XLEAP-SBS are trademarks of Illumina, Inc. Patient Test Solutions, Inc is an independent laboratory.
~100 pg
Low-input amplicon methods for limited tissue, depleted FFPE, and cell-free DNA.
Hours, not days
On-site library preparation so sequencing does not wait on a second laboratory.
This laboratory
Variant calls are reviewed and released by Patient Test Solutions, Inc — not forwarded as a raw file.
Panels
Oncology and circulating DNA, as ordered.
Targeted oncology and cfDNA panels on the current menu. Whole-exome sequencing is offered when the question is broader than a defined gene set.
| Panel | Scope | Typical use |
|---|---|---|
| Hotspot cancer panel | 50+ genes (BRAF, KRAS, EGFR and peers) | Broad solid-tumor hotspot interrogation |
| Breast cancer panel | 16 genes including BRCA1/2, AKT1, BAP1 | Breast oncology workup |
| Colorectal cancer panel | 21 genes including APC, AXIN1, AKT1 | Colorectal mutation landscape |
| Lung cancer panel | Lung-focused amplicon set | Non-small-cell and related indications |
| cfDNA / liquid biopsy | Cell-free DNA library | Plasma-based workflows |