My talk for the International Genomics session at ABRF 2017. Describing the issues caused by the uncontrolled naming of NGS methods: some examples and some suggestions about how to fix this.

1. ABRF 2017 Annual Meeting
A FORUM FOR ADVANCING TODAY’S CORE TECHNOLOGIES TO
ENABLE TOMORROW’S INNOVATIONS
March 25-28, 2017 Town and Country Resort & Convention Center
San Diego, California
A profusion of confusion in genomic methods
Dr James Hadfield
CRUK & Cambridge University

2. NGS method naming
Describe the problem
Present some examples
Suggestions on how to fix the problem
Core-facility community efforts
A genomics case report

3. NGS method naming
– 10 years of NGS
– 400 methods
– No controlled vocabulary, no convention
“What does RNA-Seq mean?”

4. Fragment)
DNA)
Quant)
DNA)
Size)select)
Size)
select)
Ligate)
adapters)
End9)
repair)
Adenylate)
Tagment)
Quant)
DNA)
Hyb)
oligos)
Extend)
ligate)
2nd)PCR)
1st)capture)
2nd)capture)
Bead)normalise)
&)pool)
Strand)
displace)
Size)select)
Circularise)
&)exo)
Bead)
purify)
Shear)
5’)ligaKon)
Reverse)
transcribe)
3’)ligaKon)
Gel)purify)
Fragment)
RNA)
2nd)strand))
dUTP)
UNG)
QC)BioAnalyser)
1st)strand)
PCR)
QT)qPCR)
Ribozero)
deplete)
Oligo)dT)
enrich)
Library)
synthesis)
Ampliy)
&)Index)
Template)
preparaKon)
QC)BioAnalyser)
QT)qPCR)TruSeq'stranded'mRNA'
TruSeq'sRNA'
TruSeq'Ribozero'
TREX'
Nextera'XT'
Nextera'
Nextera'Rapid'Exome'
Nextera'Mate2Pair'
TruSeq'ChIP,seq'
TSCA'
TruSeq'PCR,free'
TruSeq'Nano'
Thruplex'
NGS method naming
Shendure & Lieberman: The expanding scope of
DNA sequencing. Nat Biotech 2012
http://enseqlopedia.com/2013/09/finding-your-way-around-ngs-sample-prep

5. Same method different names
– MNase-Seq, MAINE-Seq and Nuc-seq
• Methods that are essentially the same are published with different names
• Suggest using MNase-Seq for all

6. Same name different methods
– Nuc-seq, Nuc-seq and sNuc-Seq
• Methods with the same names are distinct e.g. Nuc-seq is a nucleosome
positioning method, while Nuc-seq and sNuc-Seq are RNA and DNA nucleus
sequencing methods.
• Suggest using MNase-Seq, snS1Nuc-Seq, snRNA-Seq

7. Homophonic names
– CAP-seq, CapSeq, CaptureSeq or CAPP-seq(not pictured)
• Names that sound the same and lack clarity e.g. which name refers to each of
the methods for CXXC affinity purification, 5’ anchored profiling of Pol II
transcripts, targeted RNA sequencing or personalized profiling of cancer
patients.
• Suggest using CXXCaP-Seq, 5’Cap-Seq, RNAcapture-Seq

8. Is it really a new method
– ChIPmentation
• New methods are modifications of an earlier method e.g. ChIPmentation is a
low-input transposase-based ChIP-Seq method. In cases like this appending an
additional acronym may be preferable e.g. AHT-ChIP-seq, an automated high-
throughput ChIP-Seq method.
• Suggest using tnChIP-Seq

9. NGS method naming – some suggestions
1. Previously published names should used e.g. ChIP-Seq; or
modified e.g. HiChIP-Seq or TnChIP-Seq
2. Case is important: most acronyms are formed from the
method name e.g. RRBS, but the use of lowercase
characters can help pronunciation e.g. ChIP-Seq
3. Prefixes and suffixes: can be used to add information about
a method e.g. “sc” and “Bis” to denote single-cells or
bisulphite conversion, or to distinguish method variants e.g.
miCLIP-m5A, or miCLIP-m6A
4. Hyphens: can separate the method from the technology
e.g. ChIP-Seq, ChIP-qPCR & ChIP-MS or denote significant
protocol modifications e.g. PAR-CLIP-Seq

10. NGS method naming – some resources
– Discuss the problem (in press)
– Enseqlopedia – an open methods wiki (coming soon)
– Illumina methods explorer– Illumina methods explorer – closed format

11. Core-facility community efforts
– NGS mapped: finding other NGS cores
– Single-cell QC: sharing data to speed technology adoption

12. NGS mapped
http://omicsmaps.comhttp://enseqlopedia.com/ngs-mapped

13. Single-cell QC
– SCQC: a website for single-cell QC data analysis
– 10XQC: the first example

14. Single-cell QC
– Single-cell QC

15. Single-cell QC
– Single-cell QC

16. Single-cell QC
– Single-cell QC

17. Single-cell QC
– Single-cell QC

18. A genomic case report
– 3 year old with a life-threatening immunodeficiency
– Routine immunological testing was uninformative
– Presentation suggested genetic component
– Possible STAT1 mutation
• Led to debate about clinical path
• HSCT considered ineffective

19. A genomic case report
– Whole genome sequencing
• Illumina TruSeq PCR-free
• 30x coverage of trio
• Interpretation of “exome”
– NFKB1A mutation
• de novo het c.94A>G in NFKBIA
• results in IκBα serine>glycine (p.S32G where serine usually phosphorylated)
• Loss of IkBa phosphorylation prevents normal signaling via degradation
• IkBa signaling is vital adaptive and innate immune response

20. A genomic case report
– NFKB1A mutation detected by rapid WGS
– Transplant is likely to be curative
• 9/10 HLA-A-mismatched unrelated donor
• one of two patients worldwide alive with this condition
(accepted for publication)

21. Acknowledgements
– ABRF – Charlie Nicolet
– Jaques RetiefIllumina
• Steve Brumpton
• Kevin Maxwee Illumina
– James Thaventhiran
– Matt Eldridge
– My lab (Paul, Hannah, Fatimah, Marta, Ros, Johanna and Tom)
– Bioinformatics Core(particularly Rich and Anne)
– Phil Ewels SciLifeLab
– Simon Andrews Babraham
– Paul Coupland
– Marta Grzelak