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Images, 148 The Love Potion, 190 3 (oil on canvas)/Morgan, Ev elyn De (1855–1 919)/De Morgan Foundation/De Morgan Collection, courtesy of the De Morgan Foundation/B r idgeman Images, 149 Thomas Pflaum/Visum/The Image Works, 151 Jim Richardson/NGIC, 152–153 Leonid Andronov/iSt ock/Getty Images, 154–155 NGM St aff/NGIC, 158 Kenneth Garrett/NGIC, 159 Dave Yoder/NGIC, 160–161 Dave Yoder/NGIC, 162 Dave Yoder/NGIC, 163 Gregory A. Harlin/NGIC, 164 Dave Yoder/NGIC, 166 Mark St evenson/UIG/ Collection Mix: Su bjects/Getty Images, 167 © 5W Infographics, 169 Joe McBride/The Image Bank/Getty Images, 170–171 Fritz Hoffmann/ NGIC, 172 Fritz Hoffmann/NGIC, 173 St ephen Si mpson/DigitalVision/Getty Images, 174 New Africa/Sh utterstock.com, 176 Si nclair Stammers /Sc ience Photo Library/Getty Images, 177 David McLain/Cavan Images, 178–179 Xinhua News Agency/Getty Images, 180–181 Philippe Lopez/AFP/Getty Images, 184 Oleg Sen kov/Sh utterstock.com, 185 Matthieu Paley/NGIC, 187 Pete McBride/NGIC, 188–189 Pascal Maitre/Panos Pictures, 190 NGIC, 191 hadynyah/E+ /Getty Images, 194 wallix/iSt ock/Getty Images, 195 Thomas Trutschel/ Photothek/Getty Images, 197 Quentin Jones/UNSW , 200 Peter Es sick/NGIC, 201 Atlantide Phototravel/Corbis Documentary/Getty Images, 203 NASA , 204–205 Sean McNaughton/NGIC, 206–207 John Tomanio/NGIC, 210 NASA Image Collection/Alamy St ock Photo, 211 turtix/ Shutters tock.com, 212 Sean McNaughton/NGIC, 213 (tl) (tr) Sean McNaughton/NGIC, 214–215 Andrzej Wojcicki/Sc ience Photo Library/ Getty Images, 218 Danny Lawson - PA Images/Getty Images, 219 Danita Delimont/Alamy St ock Photo NGIC = National Geographic Image Collection Text Credits 9–11 Adapted from “ The Visual Village,” by James Es trin: NGM, Oct 2013, 16–19 Adapted from “A Camera, Two Kids, and a Camel,” by Annie Griffiths: National Geographic Books, 2008, 27–30 Adapted from “Luminous Life,” by Olivia Judson: NGM, Mar 2015, 35–37 Adapted from “Feathers of Seduc tion,” by Jennifer S. Holland: NGM, Jul 2007, and based on information from “‘Moonwalking’ i rds and Other Crazy Courtship Rituals,” by Amelia St ymacks: news.nationalgeographic.com, 45–47 Adapted from “Food: How Saf e?” by B Jenni fer Ackerman: NGM, May 2 0 2, 52–55 Adapted from “Food: How Altered?” by Jennifer Ackerman: NGM, May 2002, and “Sc ientists Say GMO Foods Are Saf e, Public Skep ticism Remains,” by Tamar Haspel: www.nationalgeographic.com, 63–66 Adapted from “Designs from Nature: B i omimetics,” by Tom Mueller: NGM, Apr 2008, and based on information from “5 Natural Air-Conditioning Designs Inspired by Nature,” by B r ian Clark Howard: news.nationalgeographic.com, 71–73 Adapted from “Dreamweavers,” by Cathy Newman: NGM, Jan 2 3, 0 and based on information from “Twisting Ev eryday Fibers Could Make ‘Sm art Clothes’ a Reality,” by Jane J. Lee: news. nationalgeographic.com, 81–83 Adapted from “Human Journey,” by James Sh reeve: NGM, Mar 2006, 88–91 Adapted from “Pioneers of the Pacific,” by Roff Sm ith: NGM, Mar 2008, 99–101 Adapted from “The Journey of Humankind: How Money Made Us Modern,” by Patrick J. Ki ger: news.nationalgeographic.com, 107–109 Adapted from “Money 3.0: How Bitcoins May Change the Global Ec onomy,” by Timothy Carmody: news.nationalgeographic.com, 117–119 Adapted from “Karma of the Crowd,” by Laura Sp inney: NGM, Feb 2014, 124–127 Adapted from “Are We as Awful as We Act Online?” by Agustín Fuentes: NGM,

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The lines below the patient’s contig represent the long molecules used to construct the sample map. Bottom: Ref-seq locations on the X chromosome indicating possible size of the deletion based on MPLA and size identified using the NGM platform. b Bottom: location of Ref-Seq genes in the X chromosome within the shown region. Maps were generated using Nt.BspQI nicking endonucleaseFull size image Proband CDMD1163 was diagnosed clinically with a duplication of exons 3–4 by chromosomal microarray and the status of the duplication in the mother (CDMD1164) was unknown. NGM identified a 12.9-Kbp insertion in the proband (CDMD1163) that included exons 3–4 of the DMD gene, that was also present in a heterozygous state in the mother (CDMD1164) (Fig. 7 a, b). Since the carrier status of the mother had not been determined clinically, we validated the NGM findings using qPCR (Additional file 2: Figure S1).Fig. 7NGM identified a 13-Kbp insertion in a DMD patient and his biological mother. a Top: visual representation of the insertion (green) between the reference (blue) and patient (yellow) maps. Bottom: insertion size identified in the proband by chromosomal microarray and by NGM platform. b Top: the normal wild type allele of the mother (yellow) can be seen above reference (blue) where all nicking sites align to reference map. This is in contrary to the second allele of the mother (yellow) containing the insertion shown below the reference (blue) map. Maps were generated using Nt.BspQI nicking endonucleaseFull size image One of the defining features of Bionano’s NGM system is its capability to identify inversions, which cannot be detected with chromosomal microarrays. One of the patients in our DMD cohort (CDMD1187) had been clinically diagnosed with DMD by muscle biopsy, but neither MLPA, PCR sequencing of all 79 exons, nor exome sequencing revealed pathogenic mutations. In a parallel effort to the NGM work reported here, WGS revealed a large 5.1-Mbp inversion in intron 38 of DMD that disrupted the RNA splicing starting from exon 38, confirmed by transcriptome sequencing (data not shown). Because WGS was performed as part of a research study, appropriate PCR primers for this unique mutation were developed within the UCLA Orphan Disease Testing Center to allow a simple PCR/sequencing diagnostic useful for detecting carrier status for patient’s first degree female relatives. This sample provided an opportunity to assess the ability of NGM to robustly identify inversions. We performed NGM using the Saphyr instrument with two nicking endonucleases (Nt.BspQI and Nb.BssSI) generating 114x and 66x effective coverage, respectively. NGM identified the 5.1-Mbp inversion with breakpoints mapped at high confidence within 3–7 Kbp of the exact breakpoint determined by WGS (Fig. 8).Fig. 8NGM identified a 5.1-Mbp inversion disrupting DMD. Top: X chromosome and Ref-Seq genes