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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 B4hUG/k4GUzDxZMo9qSkhvut//azK4xNn9ZEsepoCAGHBKKJtTewxYD7H/CQrj6o
 LEhUO4LyB3LRsZAJuc1b0w==

<SEC-DOCUMENT>0001005477-06-002090.txt : 20060405
<SEC-HEADER>0001005477-06-002090.hdr.sgml : 20060405
<ACCEPTANCE-DATETIME>20060405172821
ACCESSION NUMBER:		0001005477-06-002090
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060327
FILED AS OF DATE:		20060405
DATE AS OF CHANGE:		20060405

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			SEQUENOM INC
		CENTRAL INDEX KEY:			0001076481
		STANDARD INDUSTRIAL CLASSIFICATION:	SERVICES-COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH [8731]
		IRS NUMBER:				770365889
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		3595 JOHN HOPKINS CT
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		8582029000

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			PEQUOT CAPITAL MANAGEMENT INC
		CENTRAL INDEX KEY:			0001071955
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-29101
		FILM NUMBER:		06743068

	BUSINESS ADDRESS:	
		STREET 1:		500 NYALA FARM ROAD
		CITY:			WESTPORT
		STATE:			CT
		ZIP:			06880
		BUSINESS PHONE:		2034292200

	MAIL ADDRESS:	
		STREET 1:		500 NYALA FARM ROAD
		CITY:			WESTPORT
		STATE:			CT
		ZIP:			06880

	FORMER NAME:	
		FORMER CONFORMED NAME:	PEQUOT CAPITAL MANAGEMENT INC/CT/
		DATE OF NAME CHANGE:	19981118
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>edgar123.xml
<DESCRIPTION>FORM 3
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2006-03-27</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001076481</issuerCik>
        <issuerName>SEQUENOM INC</issuerName>
        <issuerTradingSymbol>SQNM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001071955</rptOwnerCik>
            <rptOwnerName>PEQUOT CAPITAL MANAGEMENT INC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>500 NYALA FARM ROAD</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WESTPORT</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06880</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Footnote 1</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, $0.001 par value</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>20000000</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Investment Advisor</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant (Right-to-buy)</value>
                <footnoteId id="F3"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.70</value>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12000000</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Investment Advisor</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Pequot Capital Management, Inc. (&quot;Pequot&quot;) is an investment advisor registered under Section 203 of the Investment Advisers Act of 1940 and has voting and investment power with respect to securities in its clients' accounts. Pequot disclaims any obligation to file this report, and this report shall not be deemed an admission that Pequot is subject to Section 16 with respect to the Issuer of such securities.  Patrick G. Enright is an employee of Pequot and will serve on the Board of Directors of the Issuer upon consummation of the transactions contemplated herein and disclaims beneficial ownership of these securities except to the extent of his pecuniary interest.</footnote>
        <footnote id="F2">Pequot disclaims beneficial ownership of these securities, and this report shall not be deemed an admission that Pequot is, for the purposes of Section 16 of the Exchange Act or otherwise, the beneficial owner of such securities.</footnote>
        <footnote id="F3">The Warrants have a term of seven years and are exercisable in whole or in part at any time after the transaction closes at an exercise price of $0.70 per share, subject to adjustment for any reverse split of the Issuer's Common Stock, certain dilutive equity issuances and for stock splits, stock dividends, mergers, reclassifications, reorganizations and other similar events.  Cashless exercise is permitted.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Aryeh Davis, GC &amp; COO, Pequot Capital Management, Inc.</signatureName>
        <signatureDate>2006-04-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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